From 4a188d135c1b76052de2d06616be6a4d2a38e262 Mon Sep 17 00:00:00 2001 From: John Duggan Date: Mon, 27 Jan 2025 16:00:54 -0500 Subject: [PATCH 1/7] Add plotly example --- code/episode_7/README.md | 0 code/episode_7/poetry.lock | 2478 +++++++++++++++++ code/episode_7/pyproject.toml | 96 + code/episode_7/src/nova_tutorial/__init__.py | 7 + code/episode_7/src/nova_tutorial/__main__.py | 5 + .../__pycache__/__init__.cpython-310.pyc | Bin 0 -> 330 bytes .../__pycache__/main.cpython-310.pyc | Bin 0 -> 491 bytes code/episode_7/src/nova_tutorial/main.py | 12 + .../__pycache__/visualization.cpython-310.pyc | Bin 0 -> 2502 bytes .../view_models/visualization.py | 59 + .../__pycache__/visualization.cpython-310.pyc | Bin 0 -> 2436 bytes .../src/nova_tutorial/views/visualization.py | 59 + 12 files changed, 2716 insertions(+) create mode 100644 code/episode_7/README.md create mode 100755 code/episode_7/poetry.lock create mode 100644 code/episode_7/pyproject.toml create mode 100644 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+python-versions = "^3.10" +content-hash = "619e22654c3ef22c2a708eb89d9310fc2cb2b48453288265d2b6de13f30c1abe" diff --git a/code/episode_7/pyproject.toml b/code/episode_7/pyproject.toml new file mode 100644 index 00000000..adf06ffd --- /dev/null +++ b/code/episode_7/pyproject.toml @@ -0,0 +1,96 @@ +[tool.poetry] +name = "nova-tutorial" +version = "0.1.0" +description = "Template application" +authors = [] +readme = "README.md" +license = "MIT" +keywords = ["NDIP", "NOVA", "python"] + +packages = [ + { include = "nova_tutorial", from = "src" } +] + + +[tool.poetry.dependencies] +python = "^3.10" +nova-galaxy = "^0.4.0" +nova-mvvm = "0.8.0" +nova-trame = "0.14.0" +pandas = "^2.2.3" +plotly = "^5.24.1" +trame-plotly = "^3.0.2" + + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" + + +[tool.pytest.ini_options] +testpaths = ["tests"] +python_files = ["test*.py"] +norecursedirs = [".git", "tmp*", "_tmp*", "__pycache__"] + +[tool.ruff] +line-length = 120 + +[tool.ruff.lint] +select = [ + "E", # pycodestyle errors + "W", # pycodestyle warnings + "F", # pyflakes + "I", # isort + "B", # flake8-bugbear + "C4", # flake8-comprehensions + "N", # PEP8 naming convetions + "D" # pydocstyle +] +ignore = [ + "C901", # too complex + "D102", # Missing docstring in public function + "D103", # Missing docstring in public method + "D401" # imperative mood + +] + +[tool.ruff.lint.extend-per-file-ignores] +'__init__.py' = ['D104'] # Missing docstring in public package + + + +[tool.ruff.lint.pydocstyle] +convention = "numpy" + +[tool.mypy] +ignore_missing_imports = false +check_untyped_defs = true +disallow_untyped_defs = true +ignore_errors = false +disable_error_code = ["import-untyped"] +# You can exclude files with the following (ONLY WHEN NECESSARY) +# exclude = ["path/to/file"] + +[tool.coverage.report] +omit = [ + '*__init__*', # __init__ files should just re-export other classes and functions +] + +[tool.coverage.run] +command_line = "-m pytest --junit-xml=reports/junit.xml" +data_file = "reports/.coverage" + +[tool.poetry.dev-dependencies] +mypy = ">=1.10.0" +pre-commit = ">=2.20.0" +coverage = ">=6.4.3" +pytest = "*" +ruff = ">=0.6.2" +copier=">=9.3" +sphinx = "*" +sphinx-rtd-theme = "*" +sphinxcontrib-napoleon ="*" +tomli = "*" + +[tool.poetry.scripts] +app = "nova_tutorial:main" diff --git a/code/episode_7/src/nova_tutorial/__init__.py b/code/episode_7/src/nova_tutorial/__init__.py new file mode 100644 index 00000000..1a91a49b --- /dev/null +++ b/code/episode_7/src/nova_tutorial/__init__.py @@ -0,0 +1,7 @@ +import importlib.metadata + +from .main import main + +__all__ = ["main"] + +__version__ = importlib.metadata.version(__package__) diff --git a/code/episode_7/src/nova_tutorial/__main__.py b/code/episode_7/src/nova_tutorial/__main__.py new file mode 100644 index 00000000..d87b5a1f --- /dev/null +++ b/code/episode_7/src/nova_tutorial/__main__.py @@ -0,0 +1,5 @@ +"""Entry point for the Package.""" + +from . import main + 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HcmV?d00001 diff --git a/code/episode_7/src/nova_tutorial/view_models/visualization.py b/code/episode_7/src/nova_tutorial/view_models/visualization.py new file mode 100644 index 00000000..3c39ad56 --- /dev/null +++ b/code/episode_7/src/nova_tutorial/view_models/visualization.py @@ -0,0 +1,59 @@ +"""View model for visualization examples.""" + +from typing import Any, Optional + +from nova.mvvm.interface import BindingInterface # type: ignore +from plotly.data import iris # type: ignore +from pydantic import BaseModel, Field, computed_field + +IRIS_DATA = iris() + + +class Plot2DOptions(BaseModel): + """Configuration for the 2D plot.""" + + axis_options: list[str] = ["sepal_length", "sepal_width", "petal_length", "petal_width", "species", "species_id"] + x_axis: str = Field(default="sepal_length", title="X Axis") + y_axis: str = Field(default="sepal_width", title="Y Axis") + z_axis: str = Field(default="petal_length", title="Z Axis") + plot_data: Any = None + plot_type: str = "scatter" + plot_type_options: list[str] = ["heatmap", "scatter"] + + @computed_field # type: ignore + @property + def is_scatter(self) -> bool: + return self.plot_type == "scatter" + + +class VisualizationViewModel: + """View model for visualization examples.""" + + def __init__(self, binding: BindingInterface): + self.config_2d = Plot2DOptions() + self.config_2d_bind = binding.new_bind(linked_object=self.config_2d, callback_after_update=self.update_2d_plot) + + def init_view(self) -> None: + self.update_2d_plot() + + def update_2d_plot(self, results: Optional[dict[str, Any]] = None) -> None: + self.config_2d.plot_data = { + "data": [ + { + "x": IRIS_DATA[self.config_2d.x_axis].tolist(), + "y": IRIS_DATA[self.config_2d.y_axis].tolist(), + "z": IRIS_DATA[self.config_2d.z_axis].tolist(), + "type": self.config_2d.plot_type, + "mode": "markers", + "colorbar": {"title": self.config_2d.z_axis}, + "colorscale": "Viridis", + } + ], + "layout": { + "title": "Iris Flower Data Set", + "xaxis": {"fixedrange": True, "title": self.config_2d.x_axis}, + "yaxis": {"fixedrange": True, "title": self.config_2d.y_axis}, + }, + } + + self.config_2d_bind.update_in_view(self.config_2d) diff --git a/code/episode_7/src/nova_tutorial/views/__pycache__/visualization.cpython-310.pyc b/code/episode_7/src/nova_tutorial/views/__pycache__/visualization.cpython-310.pyc new file mode 100644 index 0000000000000000000000000000000000000000..6201cc324ce4602d5c1a458e9c5c43f906f83ef8 GIT binary patch literal 2436 zcmd1j<>g{vU|_iTd3t&$Cj-M{5C<8vFfcGUFfcF_*Dx?Jq%cG=q%fv1^VHSyivShHb)L$ zE`Jn1n9Z3ZkSiD^$jIQ%kiwP1-NKNTEVOHVC{ zFHS8gOD)o5yv0_KlV6epGF&VS*$p7q`R1pj<|KohfQ&(b2;vtzF)%QsGDI<^Fhnt> zFh((_aJMt0F{ZGju(t3-v81r2vZgSlFsHGku%~deutc#zvR)xMC$YGgP!Qc>D@rXXEz0vtW(2tkia~6ULzzLb9l*fAP{Pp6 zuz+zP10zETQwk`qnR=OO7~+|07_ykNSZWyJSxeYT*ugxGX2xd58ishz8ioa2ARRRf zS*%&y3wUZ6vUnFVGBTtv1T$zd`$e&om8KeNGDdMH=VYelmBg1+7NlzO-C`{+El4f8 z#StH$nU`4-A78}5z`$^e4HD#0T*>))B}Mr;IjKcaEXgHBIYpo}TLg0GE!N_a#FEro zTxFT5;bxTT1@{2MP 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self.create_ui() + + # This makes the loading of the initial Trame state asynchronous, which is useful for improving the launch time + # of the application. + self.ctrl.on_server_ready.add(self.server_ready) + + def server_ready(self, **_kwargs: Any) -> None: + self.view_model.config_2d_bind.connect("config_2d") + self.view_model.init_view() + + def create_ui(self) -> None: + self.state.trame__title = "NOVA Tutorial" + with super().create_ui() as layout: + layout.pre_content.classes += "mb-4" + + with layout.content: + with GridLayout(columns=4, classes="mb-2"): + InputField(v_model="config_2d.plot_type", items="config_2d.plot_type_options", type="select") + InputField(v_model="config_2d.x_axis", items="config_2d.axis_options", type="select") + InputField(v_model="config_2d.y_axis", items="config_2d.axis_options", type="select") + InputField( + v_model="config_2d.z_axis", + disabled=("config_2d.is_scatter",), + items="config_2d.axis_options", + type="select", + ) + + with HBoxLayout(halign="center", height=400): + plotly.Figure( + v_if="config_2d.plot_data", + state_variable_name="config_2d.plot_data", + classes="h-100", + ) + + return layout -- GitLab From c58d32d83680d62274e7bbb08c46a08b29bd7931 Mon Sep 17 00:00:00 2001 From: John Duggan Date: Tue, 28 Jan 2025 15:28:10 -0500 Subject: [PATCH 2/7] Add PyVista example --- code/episode_7/poetry.lock | 530 +++++++++++++++++- code/episode_7/pyproject.toml | 2 + .../view_models/visualization.py | 24 +- .../src/nova_tutorial/views/plotly_2d.py | 33 ++ .../src/nova_tutorial/views/pyvista_3d.py | 59 ++ .../src/nova_tutorial/views/visualization.py | 30 +- 6 files changed, 653 insertions(+), 25 deletions(-) create mode 100644 code/episode_7/src/nova_tutorial/views/plotly_2d.py create mode 100644 code/episode_7/src/nova_tutorial/views/pyvista_3d.py diff --git a/code/episode_7/poetry.lock b/code/episode_7/poetry.lock index 5b3f1fcb..e4a55833 100755 --- a/code/episode_7/poetry.lock +++ b/code/episode_7/poetry.lock 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[metadata] lock-version = "2.0" python-versions = "^3.10" -content-hash = "619e22654c3ef22c2a708eb89d9310fc2cb2b48453288265d2b6de13f30c1abe" +content-hash = "f9931d7baca4d3cc5354430155449d43e5364af4fa95648bd39137bb8b05f375" diff --git a/code/episode_7/pyproject.toml b/code/episode_7/pyproject.toml index adf06ffd..fd199a7c 100644 --- a/code/episode_7/pyproject.toml +++ b/code/episode_7/pyproject.toml @@ -19,7 +19,9 @@ nova-mvvm = "0.8.0" nova-trame = "0.14.0" pandas = "^2.2.3" plotly = "^5.24.1" +pyvista = "^0.44.2" trame-plotly = "^3.0.2" +trame-vtk = "^2.8.14" [build-system] diff --git a/code/episode_7/src/nova_tutorial/view_models/visualization.py b/code/episode_7/src/nova_tutorial/view_models/visualization.py index 3c39ad56..137887e9 100644 --- a/code/episode_7/src/nova_tutorial/view_models/visualization.py +++ b/code/episode_7/src/nova_tutorial/view_models/visualization.py @@ -2,6 +2,7 @@ from typing import Any, Optional +import pyvista as pv # type: ignore from nova.mvvm.interface import BindingInterface # type: ignore from plotly.data import iris # type: ignore from pydantic import BaseModel, Field, computed_field @@ -9,7 +10,7 @@ from pydantic import BaseModel, Field, computed_field IRIS_DATA = iris() -class Plot2DOptions(BaseModel): +class PlotlyConfig(BaseModel): """Configuration for the 2D plot.""" axis_options: list[str] = ["sepal_length", "sepal_width", "petal_length", "petal_width", "species", "species_id"] @@ -17,7 +18,7 @@ class Plot2DOptions(BaseModel): y_axis: str = Field(default="sepal_width", title="Y Axis") z_axis: str = Field(default="petal_length", title="Z Axis") plot_data: Any = None - plot_type: str = "scatter" + plot_type: str = Field(default="scatter", title="Plot Type") plot_type_options: list[str] = ["heatmap", "scatter"] @computed_field # type: ignore @@ -26,15 +27,29 @@ class Plot2DOptions(BaseModel): return self.plot_type == "scatter" +class PyVistaConfig(BaseModel): + """Configuration for PyVista.""" + + colormap_options: list[str] = ["viridis", "autumn", "coolwarm", "twilight", "jet"] + opacity_options: list[str] = ["linear", "sigmoid"] + colormap: str = Field(default="viridis", title="Color Transfer Function") + opacity: str = Field(default="linear", title="Opacity Transfer Function") + + class VisualizationViewModel: """View model for visualization examples.""" def __init__(self, binding: BindingInterface): - self.config_2d = Plot2DOptions() + self.config_2d = PlotlyConfig() self.config_2d_bind = binding.new_bind(linked_object=self.config_2d, callback_after_update=self.update_2d_plot) + self.config_pyvista = PyVistaConfig() + self.config_pyvista_bind = binding.new_bind( + linked_object=self.config_pyvista, callback_after_update=self.update_pyvista + ) def init_view(self) -> None: self.update_2d_plot() + self.update_pyvista() def update_2d_plot(self, results: Optional[dict[str, Any]] = None) -> None: self.config_2d.plot_data = { @@ -57,3 +72,6 @@ class VisualizationViewModel: } self.config_2d_bind.update_in_view(self.config_2d) + + def update_pyvista(self, results: Optional[dict[str, Any]] = None) -> None: + self.config_pyvista_bind.update_in_view(self.config_pyvista) diff --git a/code/episode_7/src/nova_tutorial/views/plotly_2d.py b/code/episode_7/src/nova_tutorial/views/plotly_2d.py new file mode 100644 index 00000000..fc26d014 --- /dev/null +++ b/code/episode_7/src/nova_tutorial/views/plotly_2d.py @@ -0,0 +1,33 @@ +"""View for the 2d plot.""" + +from nova.trame.view.components import InputField # type: ignore +from nova.trame.view.layouts import GridLayout, HBoxLayout # type: ignore +from trame.widgets import plotly # type: ignore +from trame.widgets import vuetify3 as vuetify + + +class Plot2D: + """View class for the 2d plot.""" + + def __init__(self) -> None: + self.create_ui() + + def create_ui(self) -> None: + vuetify.VCardTitle("Plotly") + with GridLayout(columns=4, classes="mb-2"): + InputField(v_model="config_2d.plot_type", items="config_2d.plot_type_options", type="select") + InputField(v_model="config_2d.x_axis", items="config_2d.axis_options", type="select") + InputField(v_model="config_2d.y_axis", items="config_2d.axis_options", type="select") + InputField( + v_model="config_2d.z_axis", + disabled=("config_2d.is_scatter",), + items="config_2d.axis_options", + type="select", + ) + + with HBoxLayout(halign="center", height=400): + plotly.Figure( + v_if="config_2d.plot_data", + state_variable_name="config_2d.plot_data", + classes="h-100", + ) diff --git a/code/episode_7/src/nova_tutorial/views/pyvista_3d.py b/code/episode_7/src/nova_tutorial/views/pyvista_3d.py new file mode 100644 index 00000000..b9aaf8b1 --- /dev/null +++ b/code/episode_7/src/nova_tutorial/views/pyvista_3d.py @@ -0,0 +1,59 @@ +"""View for the 3d plot using PyVista.""" + +from typing import Any, Optional + +import pyvista as pv # type: ignore +from nova.trame.view.components import InputField # type: ignore +from nova.trame.view.layouts import GridLayout, HBoxLayout # type: ignore +from pyvista import examples +from pyvista.trame.ui import plotter_ui # type: ignore +from trame.widgets import vuetify3 as vuetify # type: ignore +from trame_server.core import Server # type: ignore + +from nova_tutorial.view_models.visualization import VisualizationViewModel + + +class PyVistaPlot: + """View class for the 3d plot using PyVista.""" + + def __init__(self, server: Server, view_model: VisualizationViewModel) -> None: + self.server = server + self.ctrl = self.server.controller + + self.view_model = view_model + + self.plotter: Optional[pv.Plotter] = None + + self.create_plotter() + self.create_ui() + + def create_plotter(self) -> None: + self.data = examples.download_knee_full() + self.plotter = pv.Plotter(off_screen=True) + + def create_ui(self) -> None: + vuetify.VCardTitle("PyVista") + with GridLayout(columns=5, classes="mb-2", valign="center"): + InputField( + v_model="config_pyvista.colormap", column_span=2, items="config_pyvista.colormap_options", type="select" + ) + InputField( + v_model="config_pyvista.opacity", column_span=2, items="config_pyvista.opacity_options", type="select" + ) + vuetify.VBtn("Render", click=self.render) + + with HBoxLayout(halign="center", height=400): + plotter_ui(self.plotter) + + def render(self, _: Any = None) -> None: + if self.plotter: + self.plotter.clear() + self.plotter.add_volume( + self.data, + cmap=self.view_model.config_pyvista.colormap, + opacity=self.view_model.config_pyvista.opacity, + show_scalar_bar=False, + ) + + self.plotter.render() + self.plotter.view_isometric() # type: ignore diff --git a/code/episode_7/src/nova_tutorial/views/visualization.py b/code/episode_7/src/nova_tutorial/views/visualization.py index cf9acd2f..009e5e09 100644 --- a/code/episode_7/src/nova_tutorial/views/visualization.py +++ b/code/episode_7/src/nova_tutorial/views/visualization.py @@ -4,12 +4,12 @@ from typing import Any from nova.mvvm.trame_binding import TrameBinding # type: ignore from nova.trame import ThemedApp # type: ignore -from nova.trame.view.components import InputField # type: ignore -from nova.trame.view.layouts import GridLayout, HBoxLayout # type: ignore from trame.app import get_server # type: ignore -from trame.widgets import plotly # type: ignore +from trame.widgets import html # type: ignore from nova_tutorial.view_models.visualization import VisualizationViewModel +from nova_tutorial.views.plotly_2d import Plot2D +from nova_tutorial.views.pyvista_3d import PyVistaPlot class VisualizationApp(ThemedApp): # Inherits from nova.trame.ThemedApp for consistent styling @@ -21,6 +21,8 @@ class VisualizationApp(ThemedApp): # Inherits from nova.trame.ThemedApp for con self.ctrl = self.server.controller self.view_model = VisualizationViewModel(TrameBinding(self.server.state)) + self.view_model.config_2d_bind.connect("config_2d") + self.view_model.config_pyvista_bind.connect("config_pyvista") self.create_ui() @@ -29,7 +31,6 @@ class VisualizationApp(ThemedApp): # Inherits from nova.trame.ThemedApp for con self.ctrl.on_server_ready.add(self.server_ready) def server_ready(self, **_kwargs: Any) -> None: - self.view_model.config_2d_bind.connect("config_2d") self.view_model.init_view() def create_ui(self) -> None: @@ -38,22 +39,9 @@ class VisualizationApp(ThemedApp): # Inherits from nova.trame.ThemedApp for con layout.pre_content.classes += "mb-4" with layout.content: - with GridLayout(columns=4, classes="mb-2"): - InputField(v_model="config_2d.plot_type", items="config_2d.plot_type_options", type="select") - InputField(v_model="config_2d.x_axis", items="config_2d.axis_options", type="select") - InputField(v_model="config_2d.y_axis", items="config_2d.axis_options", type="select") - InputField( - v_model="config_2d.z_axis", - disabled=("config_2d.is_scatter",), - items="config_2d.axis_options", - type="select", - ) - - with HBoxLayout(halign="center", height=400): - plotly.Figure( - v_if="config_2d.plot_data", - state_variable_name="config_2d.plot_data", - classes="h-100", - ) + Plot2D() + html.Div(classes="my-4") + PyVistaPlot(self.server, self.view_model) + # VTK3D() return layout -- GitLab From 6710f265fa9c1689092d228a8d1762bdfd97b4a0 Mon Sep 17 00:00:00 2001 From: John Duggan Date: Tue, 28 Jan 2025 16:02:16 -0500 Subject: [PATCH 3/7] Clean up PyVista example --- code/.gitignore | 2 ++ .../__pycache__/visualization.cpython-310.pyc | Bin 2502 -> 0 bytes .../view_models/visualization.py | 20 +++++++++++++- .../__pycache__/visualization.cpython-310.pyc | Bin 2436 -> 0 bytes .../src/nova_tutorial/views/pyvista_3d.py | 26 +++--------------- .../src/nova_tutorial/views/visualization.py | 4 +-- 6 files changed, 27 insertions(+), 25 deletions(-) create mode 100644 code/.gitignore delete mode 100644 code/episode_7/src/nova_tutorial/view_models/__pycache__/visualization.cpython-310.pyc delete mode 100644 code/episode_7/src/nova_tutorial/views/__pycache__/visualization.cpython-310.pyc diff --git a/code/.gitignore b/code/.gitignore new file mode 100644 index 00000000..a295864e --- /dev/null +++ b/code/.gitignore @@ -0,0 +1,2 @@ +*.pyc +__pycache__ diff --git a/code/episode_7/src/nova_tutorial/view_models/__pycache__/visualization.cpython-310.pyc b/code/episode_7/src/nova_tutorial/view_models/__pycache__/visualization.cpython-310.pyc deleted file mode 100644 index 35b1acd1a8b00be641c83fdb84efaebd1f70de84..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 2502 zcmd1j<>g{vU|=}+d3t&&2Lr=n5C<8vFfcGUFfcF_XD~1@q%cG=q%fv1*k_{=#hxvWvFU^Yt*TP}MPJDAOy!;#Aw#hJ?$#g)q)#m&f&%HGTn#pBM9!j{6` z!jQtA%Gt~u#p}+H!jZz+!jQt*%oN3!!WGP*$^A<$EHkxSAvZrIHAf*Wzeu4hv$!-d zC$lQCBr`uxA+;hgw;(6ASnnmst(r`?m>u&fZ*lk+fMgSMG#PIRIA!LgWag!N=9Q!t zr6ne(YBJtp$t=n&)?~iL>6BQU>I*XZ7OPukYEH^6zU2Jeg3^-Il=w6dKN(~yGG>K^ z!V(4shE#?q#uSDqrcj0y#wg}=h7_hnj8QD9tf_3045{oX%r*?E94Ra*tSM~0Oi`Sv zY^m%i>|imD6i%=h7g&r7EXJL}0~X^3i}Bhpr0_-Yr1GY+r|{b_qzFXufyD)F7*d2% 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VisualizationViewModel: def __init__(self, binding: BindingInterface): self.config_2d = PlotlyConfig() - self.config_2d_bind = binding.new_bind(linked_object=self.config_2d, callback_after_update=self.update_2d_plot) self.config_pyvista = PyVistaConfig() + self.pyvista_data = examples.download_knee_full() + + self.config_2d_bind = binding.new_bind(linked_object=self.config_2d, callback_after_update=self.update_2d_plot) self.config_pyvista_bind = binding.new_bind( linked_object=self.config_pyvista, callback_after_update=self.update_pyvista ) @@ -75,3 +78,18 @@ class VisualizationViewModel: def update_pyvista(self, results: Optional[dict[str, Any]] = None) -> None: self.config_pyvista_bind.update_in_view(self.config_pyvista) + + def render_pyvista(self, plotter: Optional[pv.Plotter]) -> None: + # TODO: This should not need to fully re-render each time. However, something about this setup is making + # view.update() not work. + if plotter: + plotter.clear() + plotter.add_volume( + self.pyvista_data, + cmap=self.config_pyvista.colormap, + opacity=self.config_pyvista.opacity, + show_scalar_bar=False, + ) + + plotter.render() + plotter.view_isometric() # type: ignore diff --git a/code/episode_7/src/nova_tutorial/views/__pycache__/visualization.cpython-310.pyc b/code/episode_7/src/nova_tutorial/views/__pycache__/visualization.cpython-310.pyc deleted file mode 100644 index 6201cc324ce4602d5c1a458e9c5c43f906f83ef8..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 2436 zcmd1j<>g{vU|_iTd3t&$Cj-M{5C<8vFfcGUFfcF_*Dx?Jq%cG=q%fv1^VHSyivShHb)L$ zE`Jn1n9Z3ZkSiD^$jIQ%kiwP1-NKNTEVOHVC{ zFHS8gOD)o5yv0_KlV6epGF&VS*$p7q`R1pj<|KohfQ&(b2;vtzF)%QsGDI<^Fhnt> zFh((_aJMt0F{ZGju(t3-v81r2vZgSlFsHGku%~deutc#zvR)xMC$YGgP!Qc>D@rXXEz0vtW(2tkia~6ULzzLb9l*fAP{Pp6 zuz+zP10zETQwk`qnR=OO7~+|07_ykNSZWyJSxeYT*ugxGX2xd58ishz8ioa2ARRRf zS*%&y3wUZ6vUnFVGBTtv1T$zd`$e&om8KeNGDdMH=VYelmBg1+7NlzO-C`{+El4f8 z#StH$nU`4-A78}5z`$^e4HD#0T*>))B}Mr;IjKcaEXgHBIYpo}TLg0GE!N_a#FEro zTxFT5;bxTT1@{2MP zbM%w*Q&RO)3o?uIQ&Qv2^^1#=!Aj%d3P3I^)<;RLdIgn5d<+Z>LZG1LVPIh3V&r4w zViaQHU=m@el0=VNJy@{ZVvo-*Pb^9=Mu|8k1_lODSa^d>lVM#R-lN zkQX$WibNS07>cAogan+B1hGUI7#QS1wu90SA0r=Ql`MuIki#6q`Jng&d7)T{k%1wF z5#;1}#uBDx29U%1%W4^G7_(Sd7_wMXn9LcN7~)xL7_->=BN-V=*i)E6*{7GOUzL%e zgd>Fwlyy=#dzryJt`zPR4mghog~yx12j=tlvM@4)Go&!EFt9K*Gcz*eaTqcbyOc9B zGJs$tDE)J$2&4$62=y}c3otU2aAk3)2&V|Ah@^;u?7`5Rgsc}swh&pihB2Ih3CZqY z21AD8CS(=hNE7p`;`Q?nb5sa{Cc7$@+$3F-m!R+lGmSKvK#`VHnwwXAiyfSbQ;VyF z;nAuGDzm`3tx6h;V0?Z7s1z**Wx1TxMpj63`l3ARXl#`lL zqzFo7O5idfIW?~&wJ37}BLjmbQxsc9Voqjy-YvF_)XemZ5)2=wB$gyrv1aHR8W?CY zN3oQ}XQo97gNuy#vc#fHkm>PxiMgpoatsU%nmk1UAbWXAKy^lZd`V_WPHGV^$Zk+h zjp8mSN{t7VMW7-8q#+8FPf9>MHjpA#5Wx;2I6=m+xn-u87NtTnP83@XxN0d911SJ! zAaLFRnXC-TJ0=Va3>=I+i~@`tOrSgj!c2@X$ni(!4<9!Rl+W>3=08(|%oiqMl~+|# z7f&y?Y6U7VRmuIG=r None: - self.server = server - self.ctrl = self.server.controller - + def __init__(self, view_model: VisualizationViewModel) -> None: self.view_model = view_model self.plotter: Optional[pv.Plotter] = None @@ -28,7 +24,6 @@ class PyVistaPlot: self.create_ui() def create_plotter(self) -> None: - self.data = examples.download_knee_full() self.plotter = pv.Plotter(off_screen=True) def create_ui(self) -> None: @@ -40,20 +35,7 @@ class PyVistaPlot: InputField( v_model="config_pyvista.opacity", column_span=2, items="config_pyvista.opacity_options", type="select" ) - vuetify.VBtn("Render", click=self.render) + vuetify.VBtn("Render", click=partial(self.view_model.render_pyvista, self.plotter)) with HBoxLayout(halign="center", height=400): plotter_ui(self.plotter) - - def render(self, _: Any = None) -> None: - if self.plotter: - self.plotter.clear() - self.plotter.add_volume( - self.data, - cmap=self.view_model.config_pyvista.colormap, - opacity=self.view_model.config_pyvista.opacity, - show_scalar_bar=False, - ) - - self.plotter.render() - self.plotter.view_isometric() # type: ignore diff --git a/code/episode_7/src/nova_tutorial/views/visualization.py b/code/episode_7/src/nova_tutorial/views/visualization.py index 009e5e09..c7d09d1a 100644 --- a/code/episode_7/src/nova_tutorial/views/visualization.py +++ b/code/episode_7/src/nova_tutorial/views/visualization.py @@ -40,8 +40,8 @@ class VisualizationApp(ThemedApp): # Inherits from nova.trame.ThemedApp for con with layout.content: Plot2D() + html.Div(classes="my-4") # visual separation between plots + PyVistaPlot(self.view_model) html.Div(classes="my-4") - PyVistaPlot(self.server, self.view_model) - # VTK3D() return layout -- GitLab From d333197aed6e7a11248d46c1f2b341f250a5b71b Mon Sep 17 00:00:00 2001 From: John Duggan Date: Tue, 28 Jan 2025 17:39:19 -0500 Subject: [PATCH 4/7] Add VTK example (needs heavy cleanup) --- code/episode_7/pyproject.toml | 1 - .../view_models/visualization.py | 106 +++++++++++++++++- .../src/nova_tutorial/views/visualization.py | 2 + .../src/nova_tutorial/views/vtk_3d.py | 47 ++++++++ 4 files changed, 153 insertions(+), 3 deletions(-) create mode 100644 code/episode_7/src/nova_tutorial/views/vtk_3d.py diff --git a/code/episode_7/pyproject.toml b/code/episode_7/pyproject.toml index fd199a7c..706779ab 100644 --- a/code/episode_7/pyproject.toml +++ b/code/episode_7/pyproject.toml @@ -23,7 +23,6 @@ pyvista = "^0.44.2" trame-plotly = "^3.0.2" trame-vtk = "^2.8.14" - [build-system] requires = ["poetry-core"] build-backend = "poetry.core.masonry.api" diff --git a/code/episode_7/src/nova_tutorial/view_models/visualization.py b/code/episode_7/src/nova_tutorial/view_models/visualization.py index f75f347f..e82d436e 100644 --- a/code/episode_7/src/nova_tutorial/view_models/visualization.py +++ b/code/episode_7/src/nova_tutorial/view_models/visualization.py @@ -2,11 +2,16 @@ from typing import Any, Optional +import numpy as np import pyvista as pv # type: ignore from nova.mvvm.interface import BindingInterface # type: ignore from plotly.data import iris # type: ignore from pydantic import BaseModel, Field, computed_field from pyvista import examples +from vtk import vtkSLCReader # type: ignore +from vtkmodules.vtkCommonDataModel import vtkPiecewiseFunction +from vtkmodules.vtkRenderingCore import vtkColorTransferFunction, vtkVolume, vtkVolumeProperty +from vtkmodules.vtkRenderingVolume import vtkFixedPointVolumeRayCastMapper IRIS_DATA = iris() @@ -43,16 +48,18 @@ class VisualizationViewModel: def __init__(self, binding: BindingInterface): self.config_2d = PlotlyConfig() self.config_pyvista = PyVistaConfig() - self.pyvista_data = examples.download_knee_full() + self.data_3d = examples.download_knee_full() self.config_2d_bind = binding.new_bind(linked_object=self.config_2d, callback_after_update=self.update_2d_plot) self.config_pyvista_bind = binding.new_bind( linked_object=self.config_pyvista, callback_after_update=self.update_pyvista ) + self.vtk_render_bind = binding.new_bind() def init_view(self) -> None: self.update_2d_plot() self.update_pyvista() + self.init_vtk() def update_2d_plot(self, results: Optional[dict[str, Any]] = None) -> None: self.config_2d.plot_data = { @@ -79,13 +86,108 @@ class VisualizationViewModel: def update_pyvista(self, results: Optional[dict[str, Any]] = None) -> None: self.config_pyvista_bind.update_in_view(self.config_pyvista) + def init_lut(self) -> vtkColorTransferFunction: + lut = vtkColorTransferFunction() + + lut.SetColorSpaceToRGB() + lut.SetNanColor([0.0, 1.0, 0.0]) + + srgb = np.array( + [ + 0, + 0.05639999999999999, + 0.05639999999999999, + 0.47, + 0.17159223942480895, + 0.24300000000000013, + 0.4603500000000004, + 0.81, + 0.2984914818394138, + 0.3568143826543521, + 0.7450246485363142, + 0.954367702893722, + 0.4321287371255907, + 0.6882, + 0.93, + 0.9179099999999999, + 0.5, + 0.8994959551205902, + 0.944646394975174, + 0.7686567142818399, + 0.5882260353170073, + 0.957107977357604, + 0.8338185108985666, + 0.5089156299842102, + 0.7061412605695164, + 0.9275207599610714, + 0.6214389091739178, + 0.31535705838676426, + 0.8476395308725272, + 0.8, + 0.3520000000000001, + 0.15999999999999998, + 1, + 0.59, + 0.07670000000000013, + 0.11947499999999994, + ] + ) + + for arr in np.split(srgb, len(srgb) / 4): # type: ignore + lut.AddRGBPoint(arr[0], arr[1], arr[2], arr[3]) + + prev_min, prev_max = lut.GetRange() + prev_delta = prev_max - prev_min + max = 200.0 + min = 75.0 + node = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0] + next_delta = max - min + for i in range(lut.GetSize()): + lut.GetNodeValue(i, node) + node[0] = next_delta * (node[0] - prev_min) / prev_delta + min + lut.SetNodeValue(i, node) + + return lut + + def init_pwf(self) -> vtkPiecewiseFunction: + pwf = vtkPiecewiseFunction() + + pwf.RemoveAllPoints() + pwf.AddPoint(75.0, 0) + pwf.AddPoint(200.0, 0.7) + + return pwf + + def init_vtk(self) -> None: + datafile = examples.download_knee_full(load=False) + reader = vtkSLCReader() + reader.SetFileName(datafile) + + mapper = vtkFixedPointVolumeRayCastMapper() + mapper.SetInputConnection(reader.GetOutputPort()) + + lut = self.init_lut() + pwf = self.init_pwf() + volume_props = vtkVolumeProperty() # type: ignore + volume_props.SetColor(lut) + volume_props.SetScalarOpacity(pwf) + volume_props.SetShade(0) + volume_props.SetInterpolationTypeToLinear() + + volume = vtkVolume() # type: ignore + volume.SetMapper(mapper) + volume.SetProperty(volume_props) + volume.SetVisibility(1) + + self.vtk_render_bind.update_in_view(volume) + def render_pyvista(self, plotter: Optional[pv.Plotter]) -> None: # TODO: This should not need to fully re-render each time. However, something about this setup is making # view.update() not work. if plotter: plotter.clear() plotter.add_volume( - self.pyvista_data, + self.data_3d, cmap=self.config_pyvista.colormap, opacity=self.config_pyvista.opacity, show_scalar_bar=False, diff --git a/code/episode_7/src/nova_tutorial/views/visualization.py b/code/episode_7/src/nova_tutorial/views/visualization.py index c7d09d1a..d8d7821f 100644 --- a/code/episode_7/src/nova_tutorial/views/visualization.py +++ b/code/episode_7/src/nova_tutorial/views/visualization.py @@ -10,6 +10,7 @@ from trame.widgets import html # type: ignore from nova_tutorial.view_models.visualization import VisualizationViewModel from nova_tutorial.views.plotly_2d import Plot2D from nova_tutorial.views.pyvista_3d import PyVistaPlot +from nova_tutorial.views.vtk_3d import VTKPlot class VisualizationApp(ThemedApp): # Inherits from nova.trame.ThemedApp for consistent styling @@ -43,5 +44,6 @@ class VisualizationApp(ThemedApp): # Inherits from nova.trame.ThemedApp for con html.Div(classes="my-4") # visual separation between plots PyVistaPlot(self.view_model) html.Div(classes="my-4") + VTKPlot(self.view_model) return layout diff --git a/code/episode_7/src/nova_tutorial/views/vtk_3d.py b/code/episode_7/src/nova_tutorial/views/vtk_3d.py new file mode 100644 index 00000000..4fc65cfe --- /dev/null +++ b/code/episode_7/src/nova_tutorial/views/vtk_3d.py @@ -0,0 +1,47 @@ +"""View for the 3d plot using PyVista.""" + +import vtkmodules.vtkInteractionWidgets # Widgets like OrientationMarkerWidget +import vtkmodules.vtkRenderingAnnotation # AxesActor and related annotations +import vtkmodules.vtkRenderingVolumeOpenGL2 # noqa +from nova.trame.view.layouts import HBoxLayout # type: ignore +from trame.widgets import vtk as vtkw # type: ignore +from trame.widgets import vuetify3 as vuetify # type: ignore +from vtkmodules.vtkInteractionStyle import vtkInteractorStyleSwitch # noqa +from vtkmodules.vtkRenderingCore import vtkRenderer, vtkRenderWindow, vtkRenderWindowInteractor, vtkVolume + +from nova_tutorial.view_models.visualization import VisualizationViewModel + + +class VTKPlot: + """View class for the 3d plot using PyVista.""" + + def __init__(self, view_model: VisualizationViewModel) -> None: + self.view_model = view_model + self.view_model.vtk_render_bind.connect(self.render) + + self.create_vtk() + self.create_ui() + + def create_vtk(self) -> None: + self.renderer = vtkRenderer() # type: ignore + self.renderer.SetBackground(0.7, 0.7, 0.7) + + self.render_window = vtkRenderWindow() + self.render_window.AddRenderer(self.renderer) + self.render_window.OffScreenRenderingOn() + + self.render_window_interactor = vtkRenderWindowInteractor() + self.render_window_interactor.SetRenderWindow(self.render_window) + self.render_window_interactor.GetInteractorStyle().SetCurrentStyleToTrackballCamera() # type: ignore + self.render_window_interactor.Initialize() # Ensure interactor is initialized + + def create_ui(self) -> None: + vuetify.VCardTitle("VTK") + + with HBoxLayout(halign="center", height=400): + self.view = vtkw.VtkRemoteView(self.render_window, interactive_ratio=1) + + def render(self, volume: vtkVolume) -> None: + self.renderer.Clear() + self.renderer.AddVolume(volume) + self.render_window.Render() -- GitLab From 10b4301c0c5102006049b3eb6b4bd6ad181f559a Mon Sep 17 00:00:00 2001 From: John Duggan Date: Wed, 29 Jan 2025 09:39:41 -0500 Subject: [PATCH 5/7] Split examples into model files --- .../src/nova_tutorial/models/plotly.py | 45 +++++ .../src/nova_tutorial/models/pyvista.py | 27 +++ .../episode_7/src/nova_tutorial/models/vtk.py | 113 +++++++++++ .../view_models/visualization.py | 178 ++---------------- .../src/nova_tutorial/views/vtk_3d.py | 5 +- 5 files changed, 198 insertions(+), 170 deletions(-) create mode 100644 code/episode_7/src/nova_tutorial/models/plotly.py create mode 100644 code/episode_7/src/nova_tutorial/models/pyvista.py create mode 100644 code/episode_7/src/nova_tutorial/models/vtk.py diff --git a/code/episode_7/src/nova_tutorial/models/plotly.py b/code/episode_7/src/nova_tutorial/models/plotly.py new file mode 100644 index 00000000..f76df468 --- /dev/null +++ b/code/episode_7/src/nova_tutorial/models/plotly.py @@ -0,0 +1,45 @@ +"""Configuration for the Plotly example.""" + +from typing import Any + +from plotly.data import iris # type: ignore +from pydantic import BaseModel, Field, computed_field + +IRIS_DATA = iris() + + +class PlotlyConfig(BaseModel): + """Configuration class for the Plotly example.""" + + axis_options: list[str] = ["sepal_length", "sepal_width", "petal_length", "petal_width", "species", "species_id"] + x_axis: str = Field(default="sepal_length", title="X Axis") + y_axis: str = Field(default="sepal_width", title="Y Axis") + z_axis: str = Field(default="petal_length", title="Z Axis") + plot_data: Any = None + plot_type: str = Field(default="scatter", title="Plot Type") + plot_type_options: list[str] = ["heatmap", "scatter"] + + @computed_field # type: ignore + @property + def is_scatter(self) -> bool: + return self.plot_type == "scatter" + + def update(self) -> None: + self.plot_data = { + "data": [ + { + "x": IRIS_DATA[self.x_axis].tolist(), + "y": IRIS_DATA[self.y_axis].tolist(), + "z": IRIS_DATA[self.z_axis].tolist(), + "type": self.plot_type, + "mode": "markers", + "colorbar": {"title": self.z_axis}, + "colorscale": "Viridis", + } + ], + "layout": { + "title": "Iris Flower Data Set", + "xaxis": {"fixedrange": True, "title": self.x_axis}, + "yaxis": {"fixedrange": True, "title": self.y_axis}, + }, + } diff --git a/code/episode_7/src/nova_tutorial/models/pyvista.py b/code/episode_7/src/nova_tutorial/models/pyvista.py new file mode 100644 index 00000000..4c9e1297 --- /dev/null +++ b/code/episode_7/src/nova_tutorial/models/pyvista.py @@ -0,0 +1,27 @@ +"""Configuration for the PyVista example.""" + +from typing import Optional + +from pydantic import BaseModel, Field +from pyvista import Plotter, examples + +KNEE_DATA = examples.download_knee_full() + + +class PyVistaConfig(BaseModel): + """Configuration class for the PyVista example.""" + + colormap_options: list[str] = ["viridis", "autumn", "coolwarm", "twilight", "jet"] + opacity_options: list[str] = ["linear", "sigmoid"] + colormap: str = Field(default="viridis", title="Color Transfer Function") + opacity: str = Field(default="linear", title="Opacity Transfer Function") + + def update(self, plotter: Optional[Plotter]) -> None: + # TODO: This should not need to fully re-render each time. However, something about this setup is making + # view.update() not work. + if plotter: + plotter.clear() + plotter.add_volume(KNEE_DATA, cmap=self.colormap, opacity=self.opacity, show_scalar_bar=False) + + plotter.render() + plotter.view_isometric() # type: ignore diff --git a/code/episode_7/src/nova_tutorial/models/vtk.py b/code/episode_7/src/nova_tutorial/models/vtk.py new file mode 100644 index 00000000..36f3d4ac --- /dev/null +++ b/code/episode_7/src/nova_tutorial/models/vtk.py @@ -0,0 +1,113 @@ +"""Configuration for the VTK example.""" + +import numpy as np +from pyvista import examples +from vtk import vtkSLCReader # type: ignore +from vtkmodules.vtkCommonDataModel import vtkPiecewiseFunction +from vtkmodules.vtkRenderingCore import vtkColorTransferFunction, vtkVolume, vtkVolumeProperty +from vtkmodules.vtkRenderingVolume import vtkFixedPointVolumeRayCastMapper + + +class VTKConfig: + """Configuration class for the VTK example.""" + + # The min/max here are somewhat arbitrary values that work well with this dataset. + max: float = 200.0 + min: float = 75.0 + + def __init__(self) -> None: + datafile = examples.download_knee_full(load=False) + reader = vtkSLCReader() + reader.SetFileName(datafile) + + mapper = vtkFixedPointVolumeRayCastMapper() + mapper.SetInputConnection(reader.GetOutputPort()) + + lut = self.init_lut() + pwf = self.init_pwf() + volume_props = vtkVolumeProperty() # type: ignore + volume_props.SetColor(lut) + volume_props.SetScalarOpacity(pwf) + volume_props.SetShade(0) + volume_props.SetInterpolationTypeToLinear() + + self.volume = vtkVolume() # type: ignore + self.volume.SetMapper(mapper) + self.volume.SetProperty(volume_props) + self.volume.SetVisibility(1) + + def get_volume(self) -> vtkVolume: + return self.volume + + def init_lut(self) -> vtkColorTransferFunction: + # This method defines the "Fast" colormap. + # See https://www.kitware.com/new-default-colormap-and-background-in-next-paraview-release/ + + lut = vtkColorTransferFunction() + + lut.SetColorSpaceToRGB() + lut.SetNanColor([0.0, 1.0, 0.0]) + + srgb = np.array( + [ + 0, + 0.05639999999999999, + 0.05639999999999999, + 0.47, + 0.17159223942480895, + 0.24300000000000013, + 0.4603500000000004, + 0.81, + 0.2984914818394138, + 0.3568143826543521, + 0.7450246485363142, + 0.954367702893722, + 0.4321287371255907, + 0.6882, + 0.93, + 0.9179099999999999, + 0.5, + 0.8994959551205902, + 0.944646394975174, + 0.7686567142818399, + 0.5882260353170073, + 0.957107977357604, + 0.8338185108985666, + 0.5089156299842102, + 0.7061412605695164, + 0.9275207599610714, + 0.6214389091739178, + 0.31535705838676426, + 0.8476395308725272, + 0.8, + 0.3520000000000001, + 0.15999999999999998, + 1, + 0.59, + 0.07670000000000013, + 0.11947499999999994, + ] + ) + + for arr in np.split(srgb, len(srgb) / 4): # type: ignore + lut.AddRGBPoint(arr[0], arr[1], arr[2], arr[3]) + + prev_min, prev_max = lut.GetRange() + prev_delta = prev_max - prev_min + node = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0] + next_delta = self.max - self.min + for i in range(lut.GetSize()): + lut.GetNodeValue(i, node) + node[0] = next_delta * (node[0] - prev_min) / prev_delta + self.min + lut.SetNodeValue(i, node) + + return lut + + def init_pwf(self) -> vtkPiecewiseFunction: + pwf = vtkPiecewiseFunction() + + pwf.RemoveAllPoints() + pwf.AddPoint(self.min, 0) + pwf.AddPoint(self.max, 0.7) + + return pwf diff --git a/code/episode_7/src/nova_tutorial/view_models/visualization.py b/code/episode_7/src/nova_tutorial/view_models/visualization.py index e82d436e..59fc8586 100644 --- a/code/episode_7/src/nova_tutorial/view_models/visualization.py +++ b/code/episode_7/src/nova_tutorial/view_models/visualization.py @@ -2,44 +2,12 @@ from typing import Any, Optional -import numpy as np -import pyvista as pv # type: ignore from nova.mvvm.interface import BindingInterface # type: ignore -from plotly.data import iris # type: ignore -from pydantic import BaseModel, Field, computed_field -from pyvista import examples -from vtk import vtkSLCReader # type: ignore -from vtkmodules.vtkCommonDataModel import vtkPiecewiseFunction -from vtkmodules.vtkRenderingCore import vtkColorTransferFunction, vtkVolume, vtkVolumeProperty -from vtkmodules.vtkRenderingVolume import vtkFixedPointVolumeRayCastMapper +from pyvista import Plotter -IRIS_DATA = iris() - - -class PlotlyConfig(BaseModel): - """Configuration for the 2D plot.""" - - axis_options: list[str] = ["sepal_length", "sepal_width", "petal_length", "petal_width", "species", "species_id"] - x_axis: str = Field(default="sepal_length", title="X Axis") - y_axis: str = Field(default="sepal_width", title="Y Axis") - z_axis: str = Field(default="petal_length", title="Z Axis") - plot_data: Any = None - plot_type: str = Field(default="scatter", title="Plot Type") - plot_type_options: list[str] = ["heatmap", "scatter"] - - @computed_field # type: ignore - @property - def is_scatter(self) -> bool: - return self.plot_type == "scatter" - - -class PyVistaConfig(BaseModel): - """Configuration for PyVista.""" - - colormap_options: list[str] = ["viridis", "autumn", "coolwarm", "twilight", "jet"] - opacity_options: list[str] = ["linear", "sigmoid"] - colormap: str = Field(default="viridis", title="Color Transfer Function") - opacity: str = Field(default="linear", title="Opacity Transfer Function") +from nova_tutorial.models.plotly import PlotlyConfig +from nova_tutorial.models.pyvista import PyVistaConfig +from nova_tutorial.models.vtk import VTKConfig class VisualizationViewModel: @@ -48,150 +16,28 @@ class VisualizationViewModel: def __init__(self, binding: BindingInterface): self.config_2d = PlotlyConfig() self.config_pyvista = PyVistaConfig() - self.data_3d = examples.download_knee_full() + self.config_vtk = VTKConfig() self.config_2d_bind = binding.new_bind(linked_object=self.config_2d, callback_after_update=self.update_2d_plot) self.config_pyvista_bind = binding.new_bind( linked_object=self.config_pyvista, callback_after_update=self.update_pyvista ) - self.vtk_render_bind = binding.new_bind() + self.config_vtk_bind = binding.new_bind() def init_view(self) -> None: self.update_2d_plot() self.update_pyvista() - self.init_vtk() + self.update_vtk() def update_2d_plot(self, results: Optional[dict[str, Any]] = None) -> None: - self.config_2d.plot_data = { - "data": [ - { - "x": IRIS_DATA[self.config_2d.x_axis].tolist(), - "y": IRIS_DATA[self.config_2d.y_axis].tolist(), - "z": IRIS_DATA[self.config_2d.z_axis].tolist(), - "type": self.config_2d.plot_type, - "mode": "markers", - "colorbar": {"title": self.config_2d.z_axis}, - "colorscale": "Viridis", - } - ], - "layout": { - "title": "Iris Flower Data Set", - "xaxis": {"fixedrange": True, "title": self.config_2d.x_axis}, - "yaxis": {"fixedrange": True, "title": self.config_2d.y_axis}, - }, - } - + self.config_2d.update() self.config_2d_bind.update_in_view(self.config_2d) def update_pyvista(self, results: Optional[dict[str, Any]] = None) -> None: self.config_pyvista_bind.update_in_view(self.config_pyvista) - def init_lut(self) -> vtkColorTransferFunction: - lut = vtkColorTransferFunction() - - lut.SetColorSpaceToRGB() - lut.SetNanColor([0.0, 1.0, 0.0]) - - srgb = np.array( - [ - 0, - 0.05639999999999999, - 0.05639999999999999, - 0.47, - 0.17159223942480895, - 0.24300000000000013, - 0.4603500000000004, - 0.81, - 0.2984914818394138, - 0.3568143826543521, - 0.7450246485363142, - 0.954367702893722, - 0.4321287371255907, - 0.6882, - 0.93, - 0.9179099999999999, - 0.5, - 0.8994959551205902, - 0.944646394975174, - 0.7686567142818399, - 0.5882260353170073, - 0.957107977357604, - 0.8338185108985666, - 0.5089156299842102, - 0.7061412605695164, - 0.9275207599610714, - 0.6214389091739178, - 0.31535705838676426, - 0.8476395308725272, - 0.8, - 0.3520000000000001, - 0.15999999999999998, - 1, - 0.59, - 0.07670000000000013, - 0.11947499999999994, - ] - ) - - for arr in np.split(srgb, len(srgb) / 4): # type: ignore - lut.AddRGBPoint(arr[0], arr[1], arr[2], arr[3]) - - prev_min, prev_max = lut.GetRange() - prev_delta = prev_max - prev_min - max = 200.0 - min = 75.0 - node = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0] - next_delta = max - min - for i in range(lut.GetSize()): - lut.GetNodeValue(i, node) - node[0] = next_delta * (node[0] - prev_min) / prev_delta + min - lut.SetNodeValue(i, node) - - return lut - - def init_pwf(self) -> vtkPiecewiseFunction: - pwf = vtkPiecewiseFunction() - - pwf.RemoveAllPoints() - pwf.AddPoint(75.0, 0) - pwf.AddPoint(200.0, 0.7) - - return pwf - - def init_vtk(self) -> None: - datafile = examples.download_knee_full(load=False) - reader = vtkSLCReader() - reader.SetFileName(datafile) - - mapper = vtkFixedPointVolumeRayCastMapper() - mapper.SetInputConnection(reader.GetOutputPort()) - - lut = self.init_lut() - pwf = self.init_pwf() - volume_props = vtkVolumeProperty() # type: ignore - volume_props.SetColor(lut) - volume_props.SetScalarOpacity(pwf) - volume_props.SetShade(0) - volume_props.SetInterpolationTypeToLinear() - - volume = vtkVolume() # type: ignore - volume.SetMapper(mapper) - volume.SetProperty(volume_props) - volume.SetVisibility(1) - - self.vtk_render_bind.update_in_view(volume) - - def render_pyvista(self, plotter: Optional[pv.Plotter]) -> None: - # TODO: This should not need to fully re-render each time. However, something about this setup is making - # view.update() not work. - if plotter: - plotter.clear() - plotter.add_volume( - self.data_3d, - cmap=self.config_pyvista.colormap, - opacity=self.config_pyvista.opacity, - show_scalar_bar=False, - ) + def render_pyvista(self, plotter: Optional[Plotter]) -> None: + self.config_pyvista.update(plotter) - plotter.render() - plotter.view_isometric() # type: ignore + def update_vtk(self) -> None: + self.config_vtk_bind.update_in_view(self.config_vtk.get_volume()) diff --git a/code/episode_7/src/nova_tutorial/views/vtk_3d.py b/code/episode_7/src/nova_tutorial/views/vtk_3d.py index 4fc65cfe..8febd410 100644 --- a/code/episode_7/src/nova_tutorial/views/vtk_3d.py +++ b/code/episode_7/src/nova_tutorial/views/vtk_3d.py @@ -1,12 +1,9 @@ """View for the 3d plot using PyVista.""" -import vtkmodules.vtkInteractionWidgets # Widgets like OrientationMarkerWidget -import vtkmodules.vtkRenderingAnnotation # AxesActor and related annotations import vtkmodules.vtkRenderingVolumeOpenGL2 # noqa from nova.trame.view.layouts import HBoxLayout # type: ignore from trame.widgets import vtk as vtkw # type: ignore from trame.widgets import vuetify3 as vuetify # type: ignore -from vtkmodules.vtkInteractionStyle import vtkInteractorStyleSwitch # noqa from vtkmodules.vtkRenderingCore import vtkRenderer, vtkRenderWindow, vtkRenderWindowInteractor, vtkVolume from nova_tutorial.view_models.visualization import VisualizationViewModel @@ -17,7 +14,7 @@ class VTKPlot: def __init__(self, view_model: VisualizationViewModel) -> None: self.view_model = view_model - self.view_model.vtk_render_bind.connect(self.render) + self.view_model.config_vtk_bind.connect(self.render) self.create_vtk() self.create_ui() -- GitLab From f2386049992e830f148bebfe76dbe1e26af2034f Mon Sep 17 00:00:00 2001 From: John Duggan Date: Wed, 29 Jan 2025 09:53:44 -0500 Subject: [PATCH 6/7] Use tabs instead of stacking the views --- .../view_models/visualization.py | 10 +++++++ .../src/nova_tutorial/views/plotly_2d.py | 15 +++++----- .../src/nova_tutorial/views/pyvista_3d.py | 3 +- .../src/nova_tutorial/views/visualization.py | 28 +++++++++++++------ .../src/nova_tutorial/views/vtk_3d.py | 2 +- 5 files changed, 40 insertions(+), 18 deletions(-) diff --git a/code/episode_7/src/nova_tutorial/view_models/visualization.py b/code/episode_7/src/nova_tutorial/view_models/visualization.py index 59fc8586..ac993ee1 100644 --- a/code/episode_7/src/nova_tutorial/view_models/visualization.py +++ b/code/episode_7/src/nova_tutorial/view_models/visualization.py @@ -3,6 +3,7 @@ from typing import Any, Optional from nova.mvvm.interface import BindingInterface # type: ignore +from pydantic import BaseModel, Field from pyvista import Plotter from nova_tutorial.models.plotly import PlotlyConfig @@ -10,14 +11,22 @@ from nova_tutorial.models.pyvista import PyVistaConfig from nova_tutorial.models.vtk import VTKConfig +class Controls(BaseModel): + """General controls for the GUI.""" + + active_tab: int = Field(default=1) + + class VisualizationViewModel: """View model for visualization examples.""" def __init__(self, binding: BindingInterface): + self.controls = Controls() self.config_2d = PlotlyConfig() self.config_pyvista = PyVistaConfig() self.config_vtk = VTKConfig() + self.controls_bind = binding.new_bind() self.config_2d_bind = binding.new_bind(linked_object=self.config_2d, callback_after_update=self.update_2d_plot) self.config_pyvista_bind = binding.new_bind( linked_object=self.config_pyvista, callback_after_update=self.update_pyvista @@ -25,6 +34,7 @@ class VisualizationViewModel: self.config_vtk_bind = binding.new_bind() def init_view(self) -> None: + self.controls_bind.update_in_view(self.controls) self.update_2d_plot() self.update_pyvista() self.update_vtk() diff --git a/code/episode_7/src/nova_tutorial/views/plotly_2d.py b/code/episode_7/src/nova_tutorial/views/plotly_2d.py index fc26d014..4fbb6ce4 100644 --- a/code/episode_7/src/nova_tutorial/views/plotly_2d.py +++ b/code/episode_7/src/nova_tutorial/views/plotly_2d.py @@ -5,11 +5,16 @@ from nova.trame.view.layouts import GridLayout, HBoxLayout # type: ignore from trame.widgets import plotly # type: ignore from trame.widgets import vuetify3 as vuetify +from nova_tutorial.view_models.visualization import VisualizationViewModel + class Plot2D: """View class for the 2d plot.""" - def __init__(self) -> None: + def __init__(self, view_model: VisualizationViewModel) -> None: + self.view_model = view_model + self.view_model.config_2d_bind.connect("config_2d") + self.create_ui() def create_ui(self) -> None: @@ -25,9 +30,5 @@ class Plot2D: type="select", ) - with HBoxLayout(halign="center", height=400): - plotly.Figure( - v_if="config_2d.plot_data", - state_variable_name="config_2d.plot_data", - classes="h-100", - ) + with HBoxLayout(halign="center", height="50vh"): + plotly.Figure(v_if="config_2d.plot_data", state_variable_name="config_2d.plot_data") diff --git a/code/episode_7/src/nova_tutorial/views/pyvista_3d.py b/code/episode_7/src/nova_tutorial/views/pyvista_3d.py index 8f1d9061..5965f961 100644 --- a/code/episode_7/src/nova_tutorial/views/pyvista_3d.py +++ b/code/episode_7/src/nova_tutorial/views/pyvista_3d.py @@ -17,6 +17,7 @@ class PyVistaPlot: def __init__(self, view_model: VisualizationViewModel) -> None: self.view_model = view_model + self.view_model.config_pyvista_bind.connect("config_pyvista") self.plotter: Optional[pv.Plotter] = None @@ -37,5 +38,5 @@ class PyVistaPlot: ) vuetify.VBtn("Render", click=partial(self.view_model.render_pyvista, self.plotter)) - with HBoxLayout(halign="center", height=400): + with HBoxLayout(halign="center", height="50vh"): plotter_ui(self.plotter) diff --git a/code/episode_7/src/nova_tutorial/views/visualization.py b/code/episode_7/src/nova_tutorial/views/visualization.py index d8d7821f..49c91464 100644 --- a/code/episode_7/src/nova_tutorial/views/visualization.py +++ b/code/episode_7/src/nova_tutorial/views/visualization.py @@ -5,7 +5,7 @@ from typing import Any from nova.mvvm.trame_binding import TrameBinding # type: ignore from nova.trame import ThemedApp # type: ignore from trame.app import get_server # type: ignore -from trame.widgets import html # type: ignore +from trame.widgets import vuetify3 as vuetify # type: ignore from nova_tutorial.view_models.visualization import VisualizationViewModel from nova_tutorial.views.plotly_2d import Plot2D @@ -22,8 +22,7 @@ class VisualizationApp(ThemedApp): # Inherits from nova.trame.ThemedApp for con self.ctrl = self.server.controller self.view_model = VisualizationViewModel(TrameBinding(self.server.state)) - self.view_model.config_2d_bind.connect("config_2d") - self.view_model.config_pyvista_bind.connect("config_pyvista") + self.view_model.controls_bind.connect("controls") self.create_ui() @@ -37,13 +36,24 @@ class VisualizationApp(ThemedApp): # Inherits from nova.trame.ThemedApp for con def create_ui(self) -> None: self.state.trame__title = "NOVA Tutorial" with super().create_ui() as layout: - layout.pre_content.classes += "mb-4" + with layout.pre_content: + with vuetify.VTabs( + v_model="controls.active_tab", classes="pl-4", update_modelValue="flushState('controls');" + ): + vuetify.VTab("Plotly", value=1) + vuetify.VTab("PyVista", value=2) + vuetify.VTab("VTK", value=3) with layout.content: - Plot2D() - html.Div(classes="my-4") # visual separation between plots - PyVistaPlot(self.view_model) - html.Div(classes="my-4") - VTKPlot(self.view_model) + with vuetify.VCard(): + with vuetify.VTabsWindow(v_model="controls.active_tab"): + with vuetify.VTabsWindowItem(value=1): + Plot2D(self.view_model) + with vuetify.VTabsWindowItem(value=2): + PyVistaPlot(self.view_model) + with vuetify.VTabsWindowItem(value=3): + VTKPlot(self.view_model) + + layout.post_content.classes += "mb-4" return layout diff --git a/code/episode_7/src/nova_tutorial/views/vtk_3d.py b/code/episode_7/src/nova_tutorial/views/vtk_3d.py index 8febd410..e5c1bed5 100644 --- a/code/episode_7/src/nova_tutorial/views/vtk_3d.py +++ b/code/episode_7/src/nova_tutorial/views/vtk_3d.py @@ -35,7 +35,7 @@ class VTKPlot: def create_ui(self) -> None: vuetify.VCardTitle("VTK") - with HBoxLayout(halign="center", height=400): + with HBoxLayout(halign="center", height="50vh"): self.view = vtkw.VtkRemoteView(self.render_window, interactive_ratio=1) def render(self, volume: vtkVolume) -> None: -- GitLab From 94cc292fcbd7e596723929d226c3e1601a56af7e Mon Sep 17 00:00:00 2001 From: John Duggan Date: Wed, 29 Jan 2025 09:59:22 -0500 Subject: [PATCH 7/7] Remove .pyc files --- .../__pycache__/__init__.cpython-310.pyc | Bin 330 -> 0 bytes .../__pycache__/main.cpython-310.pyc | Bin 491 -> 0 bytes 2 files changed, 0 insertions(+), 0 deletions(-) delete mode 100644 code/episode_7/src/nova_tutorial/__pycache__/__init__.cpython-310.pyc delete mode 100644 code/episode_7/src/nova_tutorial/__pycache__/main.cpython-310.pyc diff --git a/code/episode_7/src/nova_tutorial/__pycache__/__init__.cpython-310.pyc b/code/episode_7/src/nova_tutorial/__pycache__/__init__.cpython-310.pyc deleted file mode 100644 index 05b9add6c25247b767323643a5638fff307f9aa1..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 330 zcmd1j<>g{vU|=|MXL@=q0|Ucj5C<7EGcYhXFfcF_YcVh|q%fo~<}gGtrZA;2=P>0m zMKLilq_CtjMlq){X0a?_O=Vli7{#8#7|fu_`VwS{-%CaY1_n*WTP(SWnR!JZ!!$W= z31#LMLw=^6{O~s z6jkb$l$PWdWhUn6C+DZ6>ZcZD7U!p=#+&OG7bSz0#={lF$7kkcmc+;F6;$5hu*uC& YDa}c>1Np0%gMop8gMo*MjY)tB0GsVyegFUf diff --git a/code/episode_7/src/nova_tutorial/__pycache__/main.cpython-310.pyc b/code/episode_7/src/nova_tutorial/__pycache__/main.cpython-310.pyc deleted file mode 100644 index 43421d7a7fb42eda66824501ce3b6e0c2a8ccb35..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 491 zcmd1j<>g{vU|?W>G(G(x0|Ucj5C<7EF)%PVFfcF_>oG7eq%cG=q%fv1YPmvU zUW!6-Nn%k6L?WapF*jAAIJKxOwMg$J$Zk!>TLNL3#ifZknN^7;nfZB+1qI0<2^eN% zU|;|_%o*e`5e5c^5{71mT80{iEXD;)3qej`2xib^^wVT60x64PgP4Ac6>P00V-#~@ zLBUFfA{GV)hF|{r8Tq-X`YEO9>4|w+<@$N~Wr@1UiA4pec_l@ax+SG0`9+zDIr_=@ zDXIFY1)0V9DXH=1`o%@bV5RYJ1t1^l6;$400WsJ>P6L_G#>mH51mfM|h>r)!#K-$- zvfg5kk59=@j*pL01lb2SL=O}~#d>APz6bjOZbV*UZfbly*y%_FD+2?=Ee@O9{FKt1 aR69`k6!S1JFt9N2FmW(*uyQf7{09Iegnjk^ -- GitLab