Compare commits
3 Commits
| Author | SHA1 | Date | |
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1ced263441 | ||
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e9ea4c5248 | ||
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ae7868d410 |
@@ -38,11 +38,6 @@ If you want to cite this work, you can cite it from Zenodo:
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[](https://zenodo.org/badge/latestdoi/786623459)
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## Known Limitations
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- Only one cutter supported in EEVEE render
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- Shader fail to work when convert to mesh.
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- Section surface cannot be generated when convert to mesh (will be supported soon)
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## Roadmap
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@@ -49,15 +49,8 @@ Welcome to our [discord server](https://discord.gg/pYkNyq2TjE), if you have any
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👍 EEVEE NEXT is absolutely AWESOME! Bioxel Nodes is fully support EEVEE NEXT now! However, there are some limitations:
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👍 EEVEE NEXT is absolutely AWESOME! Bioxel Nodes is fully support EEVEE NEXT now!
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1. Only one cutter supported.
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2. EEVEE result is not that great as Cycles does.
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## Known Limitations
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- Only works with Cycles CPU , Cycles GPU (OptiX), EEVEE
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- Section surface cannot be generated when convert to mesh (will be supported soon)
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## Roadmap
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@@ -49,15 +49,7 @@ Bioxel Nodes 是一款用于科学体数据可视化的 Blender 插件。它利
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EEVEE NEXT 太棒了！Bioxel Nodes 现在全面支持 EEVEE NEXT！但仍有以下限制：
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1. 仅支持一个切割器
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2. EEVEE 渲染效果不如 Cycles
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## 已知限制
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- 仅支持 Cycles CPU、Cycles GPU (OptiX)、EEVEE
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- 转换为网格时无法生成剖面（即将支持）
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EEVEE NEXT 太棒了！Bioxel Nodes 现在全面支持 EEVEE NEXT！
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## 路线图
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@@ -1,6 +1,6 @@
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[project]
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name = "bioxelnodes"
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version = "2.0.1"
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version = "2.0.2"
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description = ""
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authors = [{ name = "MaNan", email = "icrdr2010@outlook.com" }]
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requires-python = ">=3.11.0,<3.12.dev0"
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@@ -9,6 +9,8 @@ from . import menus
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auto_load.init()
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CLI_COMMAND_NAME = "bioxelnodes_import_worker"
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def register():
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pcoll = previews.new()
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@@ -41,9 +43,11 @@ def register():
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auto_load.register()
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menus.add()
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register_cli_commands()
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def unregister():
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unregister_cli_commands()
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menus.remove()
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auto_load.unregister()
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@@ -56,3 +60,21 @@ def unregister():
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for pcoll in PREVIEW_COLLECTIONS.values():
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previews.remove(pcoll)
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PREVIEW_COLLECTIONS.clear()
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def import_worker_cli(args):
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from .operators import io_worker
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return io_worker.main(args)
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def register_cli_commands():
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unregister_cli_commands()
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bpy.utils.register_cli_command(CLI_COMMAND_NAME, import_worker_cli)
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def unregister_cli_commands():
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try:
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bpy.utils.unregister_cli_command(CLI_COMMAND_NAME)
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except Exception:
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pass
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@@ -1,7 +1,7 @@
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schema_version = "1.0.0"
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id = "bioxelnodes"
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version = "2.0.1"
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version = "2.0.2"
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name = "Bioxel Nodes"
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tagline = "For scientific volumetric data visualization in Blender"
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maintainer = "Nan <icrdr2010@outlook.com>"
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@@ -13,7 +13,7 @@ import SimpleITK as sitk
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from ..props import BIOXEL_Series
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from ..utils import get_layer_obj, wrapped_label
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from ..bioxel.parse import DICOM_EXTS, SUPPORT_EXTS, get_ext
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from ..bioxel.parse import DICOM_EXTS, SUPPORT_EXTS, get_ext, parse_volumetric_data
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from ..utils import get_cache_dir, progress_update, progress_bar
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from ..layer import get_layer_caches, set_layer_caches
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@@ -61,6 +61,14 @@ def remove_progress_bar_safe():
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pass
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def get_addon_module_name():
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package_name = __package__ or "bioxelnodes.operators"
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suffix = ".operators"
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if package_name.endswith(suffix):
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return package_name[: -len(suffix)]
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return package_name
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def start_worker_process(owner, command: str, payload: dict):
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job_dir = Path(tempfile.mkdtemp(prefix="bioxel_import_", dir=str(get_cache_dir())))
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config_path = job_dir / "config.json"
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@@ -69,24 +77,29 @@ def start_worker_process(owner, command: str, payload: dict):
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cancel_path = job_dir / "cancel"
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log_path = job_dir / "worker.log"
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addon_name = get_addon_module_name()
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config = {
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**payload,
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"command": command,
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"addon_name": addon_name,
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"progress_path": str(progress_path),
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"result_path": str(result_path),
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"cancel_path": str(cancel_path),
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}
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write_worker_json(config_path, config)
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write_worker_json(progress_path, {"factor": 0.0, "text": "Starting..."})
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write_worker_json(
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progress_path,
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{"factor": 0.0, "text": "Starting background Blender..."},
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)
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worker_path = Path(__file__).with_name("io_worker.py")
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print(f"Starting Bioxel worker with addon module: {addon_name}")
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cmd = [
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bpy.app.binary_path,
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"--background",
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"--factory-startup",
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"--python",
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str(worker_path),
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"--",
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"--addons",
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addon_name,
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"--command",
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"bioxelnodes_import_worker",
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str(config_path),
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]
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@@ -188,7 +201,6 @@ class ImportDataBase:
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context.window_manager.fileselect_add(self)
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return {"RUNNING_MODAL"}
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class ImportData(bpy.types.Operator, ImportDataBase):
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bl_idname = "bioxel.import_data"
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bl_label = "Import Data"
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@@ -291,64 +303,26 @@ class ParseVolumetricData(bpy.types.Operator):
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def execute(self, context):
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print("Collecting Meta Data...")
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self.is_cancelled = False
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self.has_error = None
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self.meta = None
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self.label_count = 0
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self.dtype = None
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progress_update(context, 0.0, "Collecting Meta Data...")
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start_worker_process(
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self,
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"read_meta",
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{
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"filepath": self.filepath,
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"series_id": self.series_id,
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},
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def progress_callback(factor, text):
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progress_update(context, factor, text)
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try:
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series_id = self.series_id if self.series_id != "empty" else ""
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data, meta = parse_volumetric_data(
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data_file=self.filepath,
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series_id=series_id,
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progress_callback=progress_callback,
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)
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except Exception as e:
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raise e
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self._timer = context.window_manager.event_timer_add(
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time_step=0.1, window=context.window
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)
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bpy.types.STATUSBAR_HT_header.append(progress_bar)
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context.window_manager.modal_handler_add(self)
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return {"RUNNING_MODAL"}
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def modal(self, context, event):
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if event.type == "ESC":
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cancel_worker_process(self, context)
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return {"PASS_THROUGH"}
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if event.type != "TIMER":
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return {"PASS_THROUGH"}
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bpy.context.workspace.status_text_set_internal(None)
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update_worker_progress(self, context)
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if self.process.poll() is None:
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return {"PASS_THROUGH"}
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context.window_manager.event_timer_remove(self._timer)
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remove_progress_bar_safe()
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self.meta = meta
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self.label_count = int(np.max(data))
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self.dtype = data.dtype
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progress_update(context, 1.0)
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result = read_worker_json(self.result_path)
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if self.is_cancelled or (result and result.get("cancelled")):
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self.report({"WARNING"}, "Canncelled by user.")
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return {"CANCELLED"}
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if not result:
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self.report({"ERROR"}, f"Import worker failed. See log: {self.log_path}")
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return {"CANCELLED"}
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if not result.get("ok"):
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print(result.get("traceback", ""))
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self.report({"ERROR"}, result.get("error", "Import worker failed."))
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return {"CANCELLED"}
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self.meta = result["meta"]
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self.label_count = int(result["label_count"])
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self.dtype = np.dtype(result["dtype"])
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for key, value in self.meta.items():
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print(f"{key}: {value}")
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@@ -1,24 +1,7 @@
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import json
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import sys
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import traceback
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from pathlib import Path
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import numpy as np
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import transforms3d
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if __package__:
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from ..bioxel.layer import Layer
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from ..bioxel.parse import parse_volumetric_data
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from ..layer import save_layers_to_cache
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else:
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PACKAGE_PARENT = Path(__file__).resolve().parents[2]
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if str(PACKAGE_PARENT) not in sys.path:
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sys.path.insert(0, str(PACKAGE_PARENT))
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from bioxelnodes.bioxel.layer import Layer
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from bioxelnodes.bioxel.parse import parse_volumetric_data
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from bioxelnodes.layer import save_layers_to_cache
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|
||||
def get_layer_shape(bioxel_size: float, orig_shape: tuple, orig_spacing: tuple):
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||||
shape = (
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@@ -72,6 +55,10 @@ def progress_callback_factory(progress_path: Path, cancel_path: Path, layer_name
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def read_meta(config, progress_path: Path, cancel_path: Path):
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||||
import numpy as np
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||||
from ..bioxel.parse import parse_volumetric_data
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progress_callback = make_progress_writer(progress_path, cancel_path)
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||||
series_id = config["series_id"] if config["series_id"] != "empty" else ""
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data, meta = parse_volumetric_data(
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@@ -94,6 +81,13 @@ def read_meta(config, progress_path: Path, cancel_path: Path):
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||||
|
||||
|
||||
def build_layers(config, progress_path: Path, cancel_path: Path):
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||||
import numpy as np
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||||
import transforms3d
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||||
|
||||
from ..bioxel.layer import Layer
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||||
from ..bioxel.parse import parse_volumetric_data
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||||
from ..layer import save_layers_to_cache
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write_json(progress_path, {"factor": 0.0, "text": "Parsing Volumetirc Data..."})
|
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progress_callback = make_progress_writer(progress_path, cancel_path, scale=0.2)
|
||||
data, meta = parse_volumetric_data(
|
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@@ -229,14 +223,19 @@ def build_layers(config, progress_path: Path, cancel_path: Path):
|
||||
return {"cache_infos": cache_infos, "added_ids": [item["id"] for item in cache_infos]}
|
||||
|
||||
|
||||
def main():
|
||||
config_path = Path(sys.argv[-1])
|
||||
def main(args):
|
||||
if not args:
|
||||
print("Usage: blender --command bioxelnodes_import_worker <config_path>")
|
||||
return 2
|
||||
|
||||
config_path = Path(args[0])
|
||||
config = json.loads(config_path.read_text(encoding="utf-8"))
|
||||
progress_path = Path(config["progress_path"])
|
||||
result_path = Path(config["result_path"])
|
||||
cancel_path = Path(config["cancel_path"])
|
||||
|
||||
try:
|
||||
write_json(progress_path, {"factor": 0.0, "text": "Loading import modules..."})
|
||||
if config["command"] == "read_meta":
|
||||
result = read_meta(config, progress_path, cancel_path)
|
||||
elif config["command"] == "import_layers":
|
||||
@@ -257,7 +256,4 @@ def main():
|
||||
"traceback": traceback.format_exc(),
|
||||
},
|
||||
)
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
main()
|
||||
return 0
|
||||
|
||||
28
uv.lock
generated
28
uv.lock
generated
@@ -25,7 +25,7 @@ wheels = [
|
||||
|
||||
[[package]]
|
||||
name = "bioxelnodes"
|
||||
version = "2.0.0"
|
||||
version = "2.0.2"
|
||||
source = { editable = "." }
|
||||
dependencies = [
|
||||
{ name = "h5py" },
|
||||
@@ -60,7 +60,7 @@ requires-dist = [
|
||||
{ name = "matplotlib", specifier = "==3.10.7" },
|
||||
{ name = "mrcfile", specifier = "==1.5.1" },
|
||||
{ name = "pyometiff", specifier = "==1.0.0" },
|
||||
{ name = "scipy", specifier = "==1.17.1" },
|
||||
{ name = "scipy", specifier = "==1.16.3" },
|
||||
{ name = "simpleitk", specifier = "==2.3.1" },
|
||||
{ name = "transforms3d", specifier = "==0.4.2" },
|
||||
]
|
||||
@@ -949,23 +949,23 @@ wheels = [
|
||||
|
||||
[[package]]
|
||||
name = "scipy"
|
||||
version = "1.17.1"
|
||||
version = "1.16.3"
|
||||
source = { registry = "https://pypi.org/simple" }
|
||||
dependencies = [
|
||||
{ name = "numpy" },
|
||||
]
|
||||
sdist = { url = "https://files.pythonhosted.org/packages/7a/97/5a3609c4f8d58b039179648e62dd220f89864f56f7357f5d4f45c29eb2cc/scipy-1.17.1.tar.gz", hash = "sha256:95d8e012d8cb8816c226aef832200b1d45109ed4464303e997c5b13122b297c0", size = 30573822, upload-time = "2026-02-23T00:26:24.851Z" }
|
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sdist = { url = "https://files.pythonhosted.org/packages/0a/ca/d8ace4f98322d01abcd52d381134344bf7b431eba7ed8b42bdea5a3c2ac9/scipy-1.16.3.tar.gz", hash = "sha256:01e87659402762f43bd2fee13370553a17ada367d42e7487800bf2916535aecb", size = 30597883, upload-time = "2025-10-28T17:38:54.068Z" }
|
||||
wheels = [
|
||||
{ url = "https://files.pythonhosted.org/packages/df/75/b4ce781849931fef6fd529afa6b63711d5a733065722d0c3e2724af9e40a/scipy-1.17.1-cp311-cp311-macosx_10_14_x86_64.whl", hash = "sha256:1f95b894f13729334fb990162e911c9e5dc1ab390c58aa6cbecb389c5b5e28ec", size = 31613675, upload-time = "2026-02-23T00:16:00.13Z" },
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{ url = "https://files.pythonhosted.org/packages/f7/58/bccc2861b305abdd1b8663d6130c0b3d7cc22e8d86663edbc8401bfd40d4/scipy-1.17.1-cp311-cp311-macosx_12_0_arm64.whl", hash = "sha256:e18f12c6b0bc5a592ed23d3f7b891f68fd7f8241d69b7883769eb5d5dfb52696", size = 28162057, upload-time = "2026-02-23T00:16:09.456Z" },
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{ url = "https://files.pythonhosted.org/packages/6d/ee/18146b7757ed4976276b9c9819108adbc73c5aad636e5353e20746b73069/scipy-1.17.1-cp311-cp311-macosx_14_0_arm64.whl", hash = "sha256:a3472cfbca0a54177d0faa68f697d8ba4c80bbdc19908c3465556d9f7efce9ee", size = 20334032, upload-time = "2026-02-23T00:16:17.358Z" },
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{ url = "https://files.pythonhosted.org/packages/ec/e6/cef1cf3557f0c54954198554a10016b6a03b2ec9e22a4e1df734936bd99c/scipy-1.17.1-cp311-cp311-macosx_14_0_x86_64.whl", hash = "sha256:766e0dc5a616d026a3a1cffa379af959671729083882f50307e18175797b3dfd", size = 22709533, upload-time = "2026-02-23T00:16:25.791Z" },
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{ url = "https://files.pythonhosted.org/packages/09/7d/af933f0f6e0767995b4e2d705a0665e454d1c19402aa7e895de3951ebb04/scipy-1.17.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:43af8d1f3bea642559019edfe64e9b11192a8978efbd1539d7bc2aaa23d92de4", size = 35349300, upload-time = "2026-02-23T00:16:49.108Z" },
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{ url = "https://files.pythonhosted.org/packages/b4/3d/7ccbbdcbb54c8fdc20d3b6930137c782a163fa626f0aef920349873421ba/scipy-1.17.1-cp311-cp311-musllinux_1_2_aarch64.whl", hash = "sha256:cd96a1898c0a47be4520327e01f874acfd61fb48a9420f8aa9f6483412ffa444", size = 35127333, upload-time = "2026-02-23T00:17:01.293Z" },
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]
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[[package]]
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||||
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||||
Reference in New Issue
Block a user