Loading pyproject.toml +1 −1 Original line number Diff line number Diff line [tool.poetry] name = "ctscan-viz" version = "0.2.1" version = "0.2.2" description = "Template application" authors = [] readme = "README.md" Loading src/ctscan_viz/models/main.py +43 −0 Original line number Diff line number Diff line """Main model.""" import os from time import time from typing import Optional import numpy as np from natsort import natsorted from pyvista import ImageData, get_reader class MainModel: Loading @@ -11,6 +15,7 @@ class MainModel: def __init__(self) -> None: self.data_directory = "" self.file_list: list[str] = [] self.volume: Optional[ImageData] = None def get_file_count(self) -> int: return len(self.file_list) Loading @@ -18,6 +23,9 @@ class MainModel: def get_file_list(self) -> list[str]: return self.file_list def get_volume(self) -> Optional[ImageData]: return self.volume def update_data_directory(self, value: str) -> None: self.data_directory = value self.update_file_list() Loading @@ -33,3 +41,38 @@ class MainModel: self.file_list = natsorted(self.file_list) except OSError: pass def update_volume(self) -> None: # Read the slices and validate their dimensions x_range = 0 y_range = 0 z_range = 0 slices = [] for path in self.file_list: start = time() slice = get_reader(path).read() slices.append(slice) z_range += 1 if x_range == 0 and y_range == 0: x_range = slice.dimensions[0] y_range = slice.dimensions[1] else: if x_range != slice.dimensions[0] or y_range != slice.dimensions[1]: raise ValueError( f"All slices must have the same dimensions. Expected {(x_range, y_range, 1)} but found " "{slice.dimensions}." ) print(f"Read slice {z_range}/{len(self.file_list)} in {time() - start:.2f}s", flush=True) # Create a numpy array from the slices start = time() scalars = np.concatenate([slice.active_scalars for slice in slices]) print(f"Numpy array creation: {time() - start:.2f}s", flush=True) start = time() # Define the 3D volume's extent self.volume = ImageData(dimensions=(x_range, y_range, z_range), origin=(0, 0, 0), spacing=(1, 1, 1)) # 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) src/ctscan_viz/view_models/main.py +32 −4 Original line number Diff line number Diff line """Main view model.""" from asyncio import create_task, sleep from threading import Thread from typing import Optional from mvvm_lib.interface import BindingInterface from pyvista import ImageData from ctscan_viz.models.main import MainModel Loading @@ -12,14 +17,36 @@ class MainViewModel: self.model = model self.binding = binding self.loading = False self.data_directory_bind = self.binding.new_bind() self.file_count_bind = self.binding.new_bind() self.render_files_bind = self.binding.new_bind() self.rendering_bind = self.binding.new_bind() self.loading_bind = self.binding.new_bind() self.render_bind = self.binding.new_bind() def get_volume(self) -> Optional[ImageData]: return self.model.get_volume() async def monitor_loading(self) -> None: while self.loading: await sleep(0.1) self.render_bind.update_in_view(None) self.update_view() def load_in_background(self) -> None: self.model.update_volume() self.loading = False def render_files(self) -> None: self.render_files_bind.update_in_view(self.model.get_file_list()) self.rendering_bind.update_in_view(False) self.loading = True self.update_view() # We run in the background to avoid blocking the main Trame thread if loading is slow. self.loading_thread = Thread(target=self.load_in_background) self.loading_thread.daemon = True self.loading_thread.start() create_task(self.monitor_loading()) def update_data_directory(self, value: str) -> None: self.model.update_data_directory(value) Loading @@ -27,3 +54,4 @@ class MainViewModel: def update_view(self) -> None: self.file_count_bind.update_in_view(self.model.get_file_count()) self.loading_bind.update_in_view(self.loading) src/ctscan_viz/views/visualization_panel.py +13 −40 Original line number Diff line number Diff line """PyVista plotter for CT scans.""" import time from time import time from typing import Any, Optional import numpy as np from pyvista import ImageData, Plotter, get_reader, start_xvfb, themes 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 Loading @@ -21,8 +21,8 @@ class VisualizationPanel: self.server = server self.vm = vm self.vm.file_count_bind.connect("file_count") self.vm.render_files_bind.connect(self.render_files) self.vm.rendering_bind.connect("rendering") self.vm.loading_bind.connect("loading") self.vm.render_bind.connect(self.render) self.plotter = self.create_plotter() self.create_ui() Loading @@ -37,49 +37,22 @@ class VisualizationPanel: def create_ui(self) -> None: @self.server.controller.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 || rendering",), click="rendering = true; trigger('start_render');", disabled=("file_count < 1 || loading",), click="trigger('start_render');", ): vuetify.VProgressCircular(indeterminate=True, v_if="rendering", size=24) 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;") def render_files(self, file_list: list[str]) -> None: self.plotter.clear() start = time.time() # Merge the slices into one 3D array x_range = 0 y_range = 0 z_range = 0 scalars = np.array([]) for path in file_list: slice_start = time.time() slice = get_reader(path).read() if len(scalars) == 0: x_range = slice.dimensions[0] y_range = slice.dimensions[1] scalars = slice.active_scalars else: scalars = np.concatenate((scalars, slice.active_scalars)) z_range += 1 print(f"Processed slice {z_range}/{len(file_list)} in {time.time() - slice_start:.2f}s", flush=True) print(f"Numpy array creation: {time.time() - start:.2f}s", flush=True) start = time.time() # Define the 3D volume's extent volume = ImageData(dimensions=(x_range, y_range, z_range), origin=(0, 0, 0), spacing=(1, 1, 1)) # Define the 3D volume's scalars for the color/opacity transfer functions volume["TIFF Scalars"] = scalars print(f"PyVista volume creation: {time.time() - start:.2f}s", flush=True) start = time.time() self.plotter.add_volume(volume, opacity="sigmoid") def render(self, _: Optional[Any] = None) -> None: start = time() self.plotter.add_volume(self.vm.get_volume(), opacity="sigmoid") self.plotter.view_isometric(self.plotter) print(f"PyVista volume rendering: {time.time() - start:.2f}s", flush=True) print(f"PyVista volume rendering: {time() - start:.2f}s", flush=True) Loading
pyproject.toml +1 −1 Original line number Diff line number Diff line [tool.poetry] name = "ctscan-viz" version = "0.2.1" version = "0.2.2" description = "Template application" authors = [] readme = "README.md" Loading
src/ctscan_viz/models/main.py +43 −0 Original line number Diff line number Diff line """Main model.""" import os from time import time from typing import Optional import numpy as np from natsort import natsorted from pyvista import ImageData, get_reader class MainModel: Loading @@ -11,6 +15,7 @@ class MainModel: def __init__(self) -> None: self.data_directory = "" self.file_list: list[str] = [] self.volume: Optional[ImageData] = None def get_file_count(self) -> int: return len(self.file_list) Loading @@ -18,6 +23,9 @@ class MainModel: def get_file_list(self) -> list[str]: return self.file_list def get_volume(self) -> Optional[ImageData]: return self.volume def update_data_directory(self, value: str) -> None: self.data_directory = value self.update_file_list() Loading @@ -33,3 +41,38 @@ class MainModel: self.file_list = natsorted(self.file_list) except OSError: pass def update_volume(self) -> None: # Read the slices and validate their dimensions x_range = 0 y_range = 0 z_range = 0 slices = [] for path in self.file_list: start = time() slice = get_reader(path).read() slices.append(slice) z_range += 1 if x_range == 0 and y_range == 0: x_range = slice.dimensions[0] y_range = slice.dimensions[1] else: if x_range != slice.dimensions[0] or y_range != slice.dimensions[1]: raise ValueError( f"All slices must have the same dimensions. Expected {(x_range, y_range, 1)} but found " "{slice.dimensions}." ) print(f"Read slice {z_range}/{len(self.file_list)} in {time() - start:.2f}s", flush=True) # Create a numpy array from the slices start = time() scalars = np.concatenate([slice.active_scalars for slice in slices]) print(f"Numpy array creation: {time() - start:.2f}s", flush=True) start = time() # Define the 3D volume's extent self.volume = ImageData(dimensions=(x_range, y_range, z_range), origin=(0, 0, 0), spacing=(1, 1, 1)) # 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)
src/ctscan_viz/view_models/main.py +32 −4 Original line number Diff line number Diff line """Main view model.""" from asyncio import create_task, sleep from threading import Thread from typing import Optional from mvvm_lib.interface import BindingInterface from pyvista import ImageData from ctscan_viz.models.main import MainModel Loading @@ -12,14 +17,36 @@ class MainViewModel: self.model = model self.binding = binding self.loading = False self.data_directory_bind = self.binding.new_bind() self.file_count_bind = self.binding.new_bind() self.render_files_bind = self.binding.new_bind() self.rendering_bind = self.binding.new_bind() self.loading_bind = self.binding.new_bind() self.render_bind = self.binding.new_bind() def get_volume(self) -> Optional[ImageData]: return self.model.get_volume() async def monitor_loading(self) -> None: while self.loading: await sleep(0.1) self.render_bind.update_in_view(None) self.update_view() def load_in_background(self) -> None: self.model.update_volume() self.loading = False def render_files(self) -> None: self.render_files_bind.update_in_view(self.model.get_file_list()) self.rendering_bind.update_in_view(False) self.loading = True self.update_view() # We run in the background to avoid blocking the main Trame thread if loading is slow. self.loading_thread = Thread(target=self.load_in_background) self.loading_thread.daemon = True self.loading_thread.start() create_task(self.monitor_loading()) def update_data_directory(self, value: str) -> None: self.model.update_data_directory(value) Loading @@ -27,3 +54,4 @@ class MainViewModel: def update_view(self) -> None: self.file_count_bind.update_in_view(self.model.get_file_count()) self.loading_bind.update_in_view(self.loading)
src/ctscan_viz/views/visualization_panel.py +13 −40 Original line number Diff line number Diff line """PyVista plotter for CT scans.""" import time from time import time from typing import Any, Optional import numpy as np from pyvista import ImageData, Plotter, get_reader, start_xvfb, themes 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 Loading @@ -21,8 +21,8 @@ class VisualizationPanel: self.server = server self.vm = vm self.vm.file_count_bind.connect("file_count") self.vm.render_files_bind.connect(self.render_files) self.vm.rendering_bind.connect("rendering") self.vm.loading_bind.connect("loading") self.vm.render_bind.connect(self.render) self.plotter = self.create_plotter() self.create_ui() Loading @@ -37,49 +37,22 @@ class VisualizationPanel: def create_ui(self) -> None: @self.server.controller.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 || rendering",), click="rendering = true; trigger('start_render');", disabled=("file_count < 1 || loading",), click="trigger('start_render');", ): vuetify.VProgressCircular(indeterminate=True, v_if="rendering", size=24) 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;") def render_files(self, file_list: list[str]) -> None: self.plotter.clear() start = time.time() # Merge the slices into one 3D array x_range = 0 y_range = 0 z_range = 0 scalars = np.array([]) for path in file_list: slice_start = time.time() slice = get_reader(path).read() if len(scalars) == 0: x_range = slice.dimensions[0] y_range = slice.dimensions[1] scalars = slice.active_scalars else: scalars = np.concatenate((scalars, slice.active_scalars)) z_range += 1 print(f"Processed slice {z_range}/{len(file_list)} in {time.time() - slice_start:.2f}s", flush=True) print(f"Numpy array creation: {time.time() - start:.2f}s", flush=True) start = time.time() # Define the 3D volume's extent volume = ImageData(dimensions=(x_range, y_range, z_range), origin=(0, 0, 0), spacing=(1, 1, 1)) # Define the 3D volume's scalars for the color/opacity transfer functions volume["TIFF Scalars"] = scalars print(f"PyVista volume creation: {time.time() - start:.2f}s", flush=True) start = time.time() self.plotter.add_volume(volume, opacity="sigmoid") def render(self, _: Optional[Any] = None) -> None: start = time() self.plotter.add_volume(self.vm.get_volume(), opacity="sigmoid") self.plotter.view_isometric(self.plotter) print(f"PyVista volume rendering: {time.time() - start:.2f}s", flush=True) print(f"PyVista volume rendering: {time() - start:.2f}s", flush=True)
