Add clim/opacity settings to fix full turbine rendering (7eb92910) · Commits · Moreland, Ken / CT Scan Visualizer

pyproject.toml

+1 −1

Original line number	Diff line number	Diff line
		[tool.poetry]
		name = "ctscan-viz"
		version = "0.2.4"
		version = "0.3.0"
		description = "Template application"
		authors = []
		readme = "README.md"

src/ctscan_viz/models/main.py

+7 −0

Original line number	Diff line number	Diff line
		@@ -15,6 +15,7 @@ class MainModel:
		def __init__(self) -> None:
		self.data_directory = ""
		self.file_list: list[str] = []
		self.needs_update = True
		self.volume: Optional[ImageData] = None

		def get_file_count(self) -> int:
		@@ -28,6 +29,7 @@ class MainModel:

		def update_data_directory(self, value: str) -> None:
		self.data_directory = value
		self.needs_update = True
		self.update_file_list()

		def update_file_list(self) -> None:
		@@ -43,6 +45,9 @@ class MainModel:
		pass

		def update_volume(self) -> None:
		if not self.needs_update:
		return

		# Read the slices and validate their dimensions
		start = time()
		x_range = 0
		@@ -76,3 +81,5 @@ class MainModel:
		# Define the 3D volume's scalars for the color/opacity transfer functions
		self.volume["TIFF Scalars"] = scalars
		print(f"PyVista volume creation: {time() - start:.2f}s", flush=True)

		self.needs_update = False

src/ctscan_viz/view_models/main.py

+40 −0

Original line number	Diff line number	Diff line
		@@ -17,17 +17,35 @@ class MainViewModel:
		self.model = model
		self.binding = binding

		self.clim_max: Optional[float] = None
		self.clim_min: Optional[float] = None
		self.loading = False
		self.opacity = "linear"

		self.clim_max_bind = self.binding.new_bind()
		self.clim_min_bind = self.binding.new_bind()
		self.data_directory_bind = self.binding.new_bind()
		self.file_count_bind = self.binding.new_bind()
		self.loading_bind = self.binding.new_bind()
		self.opacity_bind = self.binding.new_bind()
		self.render_bind = self.binding.new_bind()
		self.update_clim_bind = self.binding.new_bind()
		self.update_opacity_bind = self.binding.new_bind()

		def get_clim(self) -> Optional[list[float]]:
		if self.clim_max is None or self.clim_min is None:
		return None

		return [self.clim_min, self.clim_max]

		def get_opacity(self) -> str:
		return self.opacity

		def get_volume(self) -> Optional[ImageData]:
		return self.model.get_volume()

		async def monitor_loading(self) -> None:
		await sleep(0.1)
		while self.loading:
		await sleep(0.1)

		@@ -47,10 +65,32 @@ class MainViewModel:
		self.loading_thread.start()
		create_task(self.monitor_loading())

		def update_clim_max(self, value: str) -> None:
		try:
		self.clim_max = float(value)
		except ValueError:
		self.clim_max = None

		def update_clim_min(self, value: str) -> None:
		try:
		self.clim_min = float(value)
		except ValueError:
		self.clim_min = None

		def update_data_directory(self, value: str) -> None:
		self.model.update_data_directory(value)
		self.update_view()

		def update_loading(self, value: bool) -> None:
		self.loading = value
		self.update_view()

		def update_opacity(self, value: str) -> None:
		self.opacity = value

		def update_view(self) -> None:
		self.clim_max_bind.update_in_view(self.clim_max)
		self.clim_min_bind.update_in_view(self.clim_min)
		self.file_count_bind.update_in_view(self.model.get_file_count())
		self.loading_bind.update_in_view(self.loading)
		self.opacity_bind.update_in_view(self.opacity)

src/ctscan_viz/views/data_selector.py

+45 −3

Original line number	Diff line number	Diff line
		@@ -2,7 +2,10 @@

		from typing import Any

		from trame_facade.view.components import RemoteFileInput
		from trame.widgets import html
		from trame.widgets import vuetify3 as vuetify
		from trame_facade.view.components import InputField, RemoteFileInput
		from trame_facade.view.layouts import GridLayout
		from trame_server.core import Server

		from ctscan_viz.view_models.main import MainViewModel
		@@ -12,13 +15,18 @@ class DataSelector:
		"""Selection widget for folder containing CT scans."""

		def __init__(self, server: Server, vm: MainViewModel) -> None:
		self.server = server
		self.ctrl = server.controller
		self.vm = vm
		self.vm.clim_max_bind.connect("clim_max")
		self.vm.clim_min_bind.connect("clim_min")
		self.vm.data_directory_bind.connect("data_directory")
		self.vm.opacity_bind.connect("opacity")

		# TODO: why is this needed?
		self.last_dir = ""

		@server.change("data_directory")
		@self.server.change("data_directory")
		def _on_data_directory_change(args: Any, *kwargs: Any) -> None:
		if server.state.data_directory != self.last_dir:
		self.last_dir = server.state.data_directory
		@@ -27,11 +35,45 @@ class DataSelector:
		self.create_ui()

		def create_ui(self) -> None:
		@self.ctrl.trigger("update_clim_max")
		def _update_clim_max(value: str) -> None:
		self.vm.update_clim_max(value)

		@self.ctrl.trigger("update_clim_min")
		def _update_clim_min(value: str) -> None:
		self.vm.update_clim_min(value)

		@self.ctrl.trigger("update_opacity")
		def _update_opacity(value: str) -> None:
		self.vm.update_opacity(value)

		RemoteFileInput(
		v_model="data_directory",
		allow_files=False,
		allow_folders=True,
		base_paths=["/HFIR", "/SNS"],
		input_props={"classes": "mb-4"},
		input_props={"classes": "mb-2"},
		label="Select Data Directory",
		)

		with GridLayout(classes="mb-2", columns=4, valign="center"):
		InputField(
		v_model="clim_min",
		label="Minimum Value",
		update_modelValue="trigger('update_clim_min', [clim_min])",
		)
		InputField(
		v_model="clim_max",
		label="Maximum Value",
		update_modelValue="trigger('update_clim_max', [clim_max])",
		)
		InputField(
		v_model="opacity",
		items=("['linear', 'geom', 'sigmoid']",),
		label="Opacity",
		type="select",
		update_modelValue="trigger('update_opacity', [opacity])",
		)
		with vuetify.VBtn(disabled=("file_count < 1 \|\| loading",), click="trigger('start_render');"):
		vuetify.VProgressCircular(indeterminate=True, v_if="loading", size=24)
		html.Span("Render {{ file_count }} files", v_else=True)

src/ctscan_viz/views/visualization_panel.py

+8 −12

Original line number	Diff line number	Diff line
		@@ -6,9 +6,8 @@ from typing import Any, Optional

		from pyvista import Plotter, start_xvfb, themes
		from pyvista.trame.ui import get_viewer
		from trame.widgets import html
		from trame.widgets import vuetify3 as vuetify
		from trame_server.core import Server
		from trame_server.state import State

		from ctscan_viz.view_models.main import MainViewModel

		@@ -20,6 +19,7 @@ class VisualizationPanel:

		def __init__(self, server: Server, vm: MainViewModel) -> None:
		self.server = server
		self.ctrl = server.controller
		self.vm = vm
		self.vm.file_count_bind.connect("file_count")
		self.vm.loading_bind.connect("loading")
		@@ -28,6 +28,10 @@ class VisualizationPanel:
		self.plotter = self.create_plotter()
		self.create_ui()

		@property
		def state(self) -> State:
		return self.server.state

		def create_plotter(self) -> Plotter:
		plotter = Plotter(off_screen=True)
		plotter.background_color = "black"
		@@ -36,25 +40,17 @@ class VisualizationPanel:
		return plotter

		def create_ui(self) -> None:
		@self.server.controller.trigger("start_render")
		@self.ctrl.trigger("start_render")
		def _start_render() -> None:
		self.plotter.clear()
		self.vm.render_files()

		view = get_viewer(self.plotter)

		with vuetify.VBtn(
		classes="mb-2",
		disabled=("file_count < 1 \|\| loading",),
		click="trigger('start_render');",
		):
		vuetify.VProgressCircular(indeterminate=True, v_if="loading", size=24)
		html.Span("Render {{ file_count }} files", v_else=True)
		view.ui(mode="server", style="height: 66vh;")

		async def render_in_background(self) -> None:
		start = time()
		self.plotter.add_volume(self.vm.get_volume(), opacity="sigmoid")
		self.plotter.add_volume(self.vm.get_volume(), clim=self.vm.get_clim(), opacity=self.vm.get_opacity())
		self.plotter.view_isometric(self.plotter)
		print(f"PyVista volume rendering: {time() - start:.2f}s", flush=True)