Merge pull request #9 from OmooLab/feature/dev

fix: save all node path not right

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 OmooLab
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -1,3 +1,110 @@
-# BioxelNodes
-BioxelNodes is a blender add-on for better volume data visualization with cycles.
+[中文文档](https://uj6xfhbzp0.feishu.cn/wiki/Qx3VwHuNPimeI8kr6nDcvl1DnHf?from=from_copylink)
 
+# Bioxel Nodes
+
+![Static Badge](https://img.shields.io/badge/Blender-orange?style=for-the-badge&logo=blender&logoColor=white)
+![GitHub License](https://img.shields.io/github/license/OmooLab/BioxelNodes?style=for-the-badge)
+![GitHub Release](https://img.shields.io/github/v/release/OmooLab/BioxelNodes?style=for-the-badge)
+![GitHub Repo stars](https://img.shields.io/github/stars/OmooLab/BioxelNodes?style=for-the-badge)
+
+Bioxel Nodes is a Blender add-on for scientific volumetric data visualization. It using Blender's powerful Geometry Nodes | Cycles to process and render volumetric data.
+
+# About
+
+Before us, there have been many tutorials and add-ons for importing volumetric data into Blender. However, we found that there were many details that were not addressed in place, some scientific facts were ignored, and the volume rendering was not pretty enough. With Bioxel Nodes, you can easily import the volumetric data into Blender, and more importantly, it can quickly make a beautiful realistic rendering of it.
+
+Below are some examples with Bioxel Nodes. Thanks to Cycles Render, the volumetric data can be rendered with great detail:
+
+![gallery](docs/images/gallery.png)
+
+### Known limitations
+
+- Cannot read DICOM with multiple series.
+- Sections cannot be generated
+- Only sequence files are supported, packed volume data formats are not supported yet (will be supported soon)
+
+# Getting Started
+
+Currently only support Blender 4.1 or above, make sure you have the correct version of Blender.
+
+### Add-on Installation
+
+Download the latest version https://github.com/OmooLab/BioxelNodes/releases/latest  
+In Blender, `Edit - Preferences - Add-ons - Install`, select the `BioxelNodes_{version}.zip` you just downloaded.
+
+### Dependency Installation
+
+The add-on requires a third-party python dependency called SimpleITK, click the Install SimpleITK button below to install the dependency. After clicking, blender may get stuck, it is downloading and installing, just wait for a moment. After the Installation, **restart blender once**.
+
+![dependency](docs/images/dependency.png)
+
+This step may have failed due to network factors, just click "Set PyPI Mirror" to change the mirror.
+
+### Basic Usage
+
+First you need to have your volumetric data ready. If not, you can access open research data from [Dryad](https://datadryad.org) (Dryad publishes data exclusively under a [Creative Commons Public Domain License](https://creativecommons.org/public-domain/cc0/))
+
+Note: Make sure one folder contains only one sequence, multiple sequences need to be manually split into different folders first.
+
+In Blender, `File - Import - Volume Data as Bioxels`, select **one** of the .dcm files and click on "Volume Data as Bioxels" (you can also drag one of the .dcm files directly into the 3D viewport to trigger the import, but this is limited to .dcm format files)
+
+![importing](docs/images/importing.png)
+
+It may take a while to read data. After finishing reading, it will pop up a dialog box
+
+![import dialog](docs/images/import_dialog.png)
+
+Ignore the options, just click OK!
+
+After importing, the necessary nodes are automatically added, the reconstruction and shader are created, and then turned on the cycles rendering to directly see the result.
+
+![result](docs/images/result.png)
+
+Click select Bioxels Object, and open the Geometry Nodes panel to see the following node graph:
+
+![segment node](docs/images/segment_node.png)
+
+You can change the "Threshold" to modify the reconstruction model, or change the "Color", "Density" to modify the shader effect. All the parameters are straightforward, you can understand them by changing the values.
+
+The node, that named "Segment", is a preset node that combines the steps of 3D reconstruction process and shading process. In general, you need to add one of the segmentation node to reconstruction first, and followed by one of the shader node to set the shader. As you can see in the following figure:
+
+![general graph](docs/images/general_graph.png)
+
+Currently there are 3 types of nodes
+
+- Segmentation nodes, responsible for splitting the volume into a reconstructed model (we call them "Segment").
+- Shader nodes, responsible for giving shader to the Segment.
+- Slicer nodes, responsible for partially cutting the Segment.
+
+For example:
+
+![general graph example](docs/images/general_graph_example.png)
+
+You can add a "Bake" node between segmentation node and shader node, if the reconstruction process consumes too much computing time. But be sure, you are selecting the volume object, not the container object.
+
+![bake node](docs/images/bake_node.png)
+
+# Future Features
+
+- Support more volumetric data formats (.nii, .map, .txm...)
+- Generate sections
+- More segmentation methods, e.g. AI segmentation.
+- Even better shader for volumetric rendering
+
+# Technical Notes
+
+The "Bioxel" in "BioxelNodes", is a combination of the words "Bio-" and "Voxel". Bioxel is a voxel that stores biological data, so maybe its chinese name should be "生素" 😂? The volumetric data made up of Bioxel is called Bioxels. We are developing a toolkit around Bioxels for better biological data visualization. but before its release, we made this Blender version of bioxels toolkit first, in order to let more people to have fun with volumetric data. 
+
+### Bioxels
+
+Bioxels is based on the RAS coordinate system, Right Aanterior Superior, which was chosen over LPS because it is more compatible with most 3D CG software coordinate systems, and is in line with the 3D artist's understanding of space.
+
+All distances within Bioxels are in Units, and are specified in Meter pre unit. However, when Bioxels is imported into 3D CG software, its size in the software is not scaled by reading the Meter pre unit directly. The reason for this is that many 3D operations in software require that the primtives not be too large or too small.
+
+### Based on OpenVDB
+
+Bioxels is based entirely on OpenVDB for storage and rendering. The main reason for choosing OpenVDB is that as a volumetric data format, it is the fastest way to work with most CG renderers.
+
+### Based on Geometry Nodes
+
+Bioxel Nodes relies on Blender Geometry Nodes to reconstruct and render volumetric data. Node-based operations ensure that the original data is not permanently altered during reconstruction and rendering operations. The fact that the processing is based on Geometry Nodes without any additional dependencies also ensures that Blender can open files without this plugin installed. Look for more support for OpenVDB in GeometryNodes so that Bioxel Nodes can do more in the future.

bioxelnodes/__init__.py

@@ -6,18 +6,24 @@ import bpy
 
 
 bl_info = {
-    "name": "BiovelNodes",
+    "name": "Bioxel Nodes",
     "author": "Ma Nan",
     "description": "",
-    "blender": (4, 0, 0),
+    "blender": (4, 1, 0),
     "version": (0, 1, 0),
     "location": "File -> Import",
     "warning": "",
-    "category": "Import-Export"
+    "category": "Node"
 }
 
 auto_load.init()
 
+bpy.types.Scene.bioxels_dir = bpy.props.StringProperty(
+    name="Bioxels Directory",
+    subtype='DIR_PATH',
+    default="//"
+)
+
 
 def register():
     auto_load.register()

bioxelnodes/convert.py

@@ -1,5 +1,5 @@
 import bpy
-from .utils import get_bioxels_obj
+from .utils import get_bioxels_obj, get_node_by_type
 
 
 class ConvertToMesh(bpy.types.Operator):
@@ -8,6 +8,15 @@ class ConvertToMesh(bpy.types.Operator):
     bl_description = "Convert Bioxels To Mesh."
     bl_options = {'UNDO'}
 
+    @classmethod
+    def poll(cls, context):
+        bioxels_obj = None
+        for obj in bpy.context.selected_objects:
+            bioxels_obj = get_bioxels_obj(obj)
+            break
+
+        return True if bioxels_obj else False
+
     def execute(self, context):
         bioxels_objs = []
 
@@ -16,7 +25,7 @@ class ConvertToMesh(bpy.types.Operator):
             if bioxels_obj:
                 bioxels_objs.append(bioxels_obj)
 
-        if len(bioxels_objs)==0:
+        if len(bioxels_objs) == 0:
             self.report({"WARNING"}, "Cannot find any bioxels.")
             return {'FINISHED'}
 
@@ -31,7 +40,7 @@ class ConvertToMesh(bpy.types.Operator):
             nodes = modifier.node_group.nodes
             links = modifier.node_group.links
 
-            output_node = nodes.get("Group Output")
+            output_node = get_node_by_type(nodes, 'NodeGroupOutput')[0]
             object_node = nodes.new("GeometryNodeObjectInfo")
             realize_nodes = nodes.new("GeometryNodeRealizeInstances")
             object_node.inputs[0].default_value = bioxels_obj
@@ -43,4 +52,6 @@ class ConvertToMesh(bpy.types.Operator):
             bpy.context.object.active_material_index = 1
             bpy.ops.object.material_slot_remove()
 
+            self.report({"INFO"}, f"Successfully convert to mesh")
+
         return {'FINISHED'}

bioxelnodes/custom_nodes/__init__.py

@@ -1 +0,0 @@
-from .node_menu import CustomNodes

bioxelnodes/customnodes/__init__.py

@@ -0,0 +1 @@
+from .menu import CustomNodes

bioxelnodes/customnodes/menu.py

@@ -1,7 +1,65 @@
+import shutil
 import bpy
 from pathlib import Path
 from .nodes import AddCustomNode
 
+bpy.types.Scene.custom_nodes_dir = bpy.props.StringProperty(
+    name="Nodes Directory",
+    subtype='DIR_PATH',
+    default="//"
+)
+
+
+class SaveAllNodes(bpy.types.Operator):
+    bl_idname = "customnodes.save_all_nodes"
+    bl_label = "Save All Custom Nodes"
+    bl_description = "Save All Custom Nodes to Directory."
+    bl_options = {'UNDO'}
+
+    def execute(self, context):
+        files = []
+        for classname in dir(bpy.types):
+            if "CUSTOMNODES_MT_NODES_" in classname:
+                cls = getattr(bpy.types, classname)
+                files.append(cls.nodes_file)
+        files = list(set(files))
+
+        for file in files:
+            file_name = Path(file).name
+            # "//"
+            custom_nodes_dir = bpy.path.abspath(context.scene.custom_nodes_dir)
+
+            output_path: Path = Path(custom_nodes_dir, file_name).resolve()
+            source_path: Path = Path(file).resolve()
+
+            if output_path != source_path:
+                shutil.copy(source_path, output_path)
+
+            for lib in bpy.data.libraries:
+                lib_path = str(Path(bpy.path.abspath(lib.filepath)).resolve())
+                if lib_path == file:
+                    blend_path = Path(bpy.path.abspath("//")).resolve()
+                    lib.filepath = bpy.path.relpath(
+                        str(output_path), start=str(blend_path))
+
+            self.report({"INFO"}, f"Successfully saved to {output_path}")
+
+        return {'FINISHED'}
+
+
+class CUSTOMNODES_PT_CustomNodes(bpy.types.Panel):
+    bl_idname = "CUSTOMNODES_PT_CustomNodes"
+    bl_label = "Custom Nodes"
+    bl_space_type = "PROPERTIES"
+    bl_region_type = "WINDOW"
+    bl_context = "scene"
+
+    def draw(self, context):
+        layout = self.layout
+        scene = context.scene
+        layout.prop(scene, 'custom_nodes_dir')
+        layout.operator(SaveAllNodes.bl_idname)
+
 
 class CustomNodes():
     def __init__(
@@ -12,10 +70,10 @@ class CustomNodes():
         root_icon='NONE'
     ) -> None:
         if not Path(nodes_file).is_file():
-            raise FileNotFoundError(Path(nodes_file).resolve().as_posix())
+            raise FileNotFoundError(str(Path(nodes_file).resolve()))
 
         self.menu_items = menu_items
-        self.nodes_file = Path(nodes_file).resolve().as_posix()
+        self.nodes_file = str(Path(nodes_file).resolve())
 
         self.root_label = root_label
         self.root_icon = root_icon
@@ -28,7 +86,7 @@ class CustomNodes():
         )
         self.menu_classes = menu_classes
 
-        idname = f"CUSTOMNODES_MT_NODES__{root_label.replace(' ', '').upper()}"
+        idname = f"CUSTOMNODES_MT_NODES_{root_label.replace(' ', '').upper()}"
 
         def add_node_menu(self, context):
             if ('GeometryNodeTree' == bpy.context.area.spaces[0].tree_type):
@@ -40,7 +98,7 @@ class CustomNodes():
 
     def _create_menu_class(self, menu_classes, items, label='CustomNodes', icon=0, idname_namespace=None):
         nodes_file = self.nodes_file
-        idname_namespace = idname_namespace or "CUSTOMNODES_MT_NODES_"
+        idname_namespace = idname_namespace or "CUSTOMNODES_MT_NODES"
         idname = f"{idname_namespace}_{label.replace(' ', '').upper()}"
 
         # create submenu class if item is menu.
@@ -60,6 +118,7 @@ class CustomNodes():
         class Menu(bpy.types.Menu):
             bl_idname = idname
             bl_label = label
+            nodes_file = self.nodes_file
 
             def draw(self, context):
                 layout = self.layout

bioxelnodes/externalpackage/package.py

@@ -231,7 +231,7 @@ class PackageInstaller():
         """
 
         # path to python.exe
-        python_exe = Path(sys.executable).resolve().as_posix()
+        python_exe = str(Path(sys.executable).resolve())
 
         # build the command list
         cmd_list = [python_exe] + cmd_list
@@ -373,7 +373,7 @@ class EXTERNALPACKAGE_OT_Install_Package(bpy.types.Operator):
         )
 
         result = installer.install_package(f"{self.package}=={self.version}")
-        if result.returncode == 0 and installer.is_installed(self.package):
+        if result.returncode == 0 or installer.is_installed(self.package):
             self.report(
                 {'INFO'},
                 f"Successfully installed {self.package} v{self.version}"
@@ -381,9 +381,7 @@ class EXTERNALPACKAGE_OT_Install_Package(bpy.types.Operator):
         else:
             self.report(
                 {'ERROR'},
-                f"""
-Error installing package. Please check the log files
-in {preferences.log_dir}.
-                """
+                f"""Error installing package. Please check the log files
+in {preferences.log_dir}."""
             )
         return {'FINISHED'}

bioxelnodes/externalpackage/preferences.py

@@ -14,13 +14,13 @@ class ExternalPackagePreferences():
     requirements_dir: bpy.props.StringProperty(
         name="requirements.txt Directory",
         subtype='DIR_PATH',
-        default=Path(__file__).parent.as_posix()
+        default=str(Path(__file__).parent)
     )  # type: ignore
 
     log_dir: bpy.props.StringProperty(
         name="Python Log Directory",
         subtype='DIR_PATH',
-        default=Path(Path.home(), '.externalpackage', 'logs').as_posix()
+        default=str(Path(Path.home(), '.externalpackage', 'logs'))
     )  # type: ignore
 
     pypi_mirror_provider: bpy.props.StringProperty(
@@ -40,7 +40,6 @@ class ExternalPackagePreferences():
         row_import = col_main.row()
         row_import.prop(self, 'pypi_mirror_provider', text='Set PyPI Mirror')
 
-        
         installer = PackageInstaller(
             pypi_mirror_provider=self.pypi_mirror_provider,
             log_dir=self.log_dir,

bioxelnodes/io.py

@@ -6,7 +6,7 @@ import numpy as np
 from pathlib import Path
 from uuid import uuid4
 import mathutils
-from .utils import calc_bbox_verts, extract_last_number, get_bioxels_obj, show_message
+from .utils import calc_bbox_verts, extract_last_number, get_bioxels_obj, get_node_by_type, show_message
 from .nodes import custom_nodes
 
 SUPPORT_EXTS = ['.dcm', '.tif', '.tiff', '.png', '.bmp', '', '.jpg']
@@ -23,7 +23,7 @@ def get_data_files(filepath: str):
         return extract_last_number(file.stem)
 
     files.sort(key=last_number)
-    files = [f.as_posix() for f in files]
+    files = [str(f) for f in files]
     return files
 
 
@@ -69,8 +69,8 @@ def on_info_changed(self, context):
 
 class ImportDICOMDialog(bpy.types.Operator):
     bl_idname = "bioxelnodes.import_dicom_dialog"
-    bl_label = "Volume Data as Biovels"
-    bl_description = "Import Volume Data as Biovels (VDB)."
+    bl_label = "Volume Data as Bioxels"
+    bl_description = "Import Volume Data as Bioxels (VDB)."
     bl_options = {'UNDO'}
 
     filepath: bpy.props.StringProperty(
@@ -79,7 +79,7 @@ class ImportDICOMDialog(bpy.types.Operator):
     )  # type: ignore
 
     bioxels_shape: bpy.props.IntVectorProperty(
-        name="Bioxels Shape",
+        name="Bioxels Shape (ReadOnly)",
         min=0,
         default=(100, 100, 100)
     )  # type: ignore
@@ -128,23 +128,13 @@ class ImportDICOMDialog(bpy.types.Operator):
     )  # type: ignore
 
     def execute(self, context):
-        if not self.filepath:
-            self.report({"WARNING"}, "Get no file path.")
-            return {'CANCELLED'}
-
-        if Path(self.filepath).suffix not in SUPPORT_EXTS:
-            self.report({"WARNING"}, "Not Supported extension.")
-            return {'CANCELLED'}
-
-        file_path = Path(self.filepath).resolve()
-        name = file_path.parent.name
         files = get_data_files(self.filepath)
+        name = Path(self.filepath).parent.name
 
         import SimpleITK as sitk
         image = sitk.ReadImage(files)
 
         bioxel_size = float(self.bioxel_size)
-
         orig_spacing = tuple(self.orig_spacing)
         image_spacing = image.GetSpacing()
         image_shape = image.GetSize()
@@ -161,9 +151,6 @@ class ImportDICOMDialog(bpy.types.Operator):
             int(image_shape[2] / bioxel_size * orig_spacing[2]),
         )
 
-        print("Bioxel Size:", bioxel_size)
-        print("Bioxels Shape:", bioxels_shape)
-
         print("Resampling...")
         image = sitk.Resample(
             image1=image,
@@ -177,14 +164,12 @@ class ImportDICOMDialog(bpy.types.Operator):
             outputPixelType=image.GetPixelID(),
         )
 
-        try:
-            image = sitk.DICOMOrient(image, 'RAS')
-        except:
-            ...
+        print("Orienting to RAS...")
+        image = sitk.DICOMOrient(image, 'RAS')
 
         array = sitk.GetArrayFromImage(image)
         orig_dtype = str(array.dtype)
-        print(f"Coverting Dtype {orig_dtype} -> float")
+        print(f"Coverting Dtype from {orig_dtype} to float...")
         array = array.astype(float)
 
         # ITK indices, by convention, are [i,j,k] while NumPy indices are [k,j,i]
@@ -198,6 +183,10 @@ class ImportDICOMDialog(bpy.types.Operator):
         array = np.transpose(array)
         bioxels_max = float(np.max(array))
         bioxels_min = float(np.min(array))
+        bioxels_shape = array.shape
+
+        print("Bioxel Size:", bioxel_size)
+        print("Bioxels Shape:", bioxels_shape)
 
         bioxels_offset = 0.0
         if bioxels_min < 0 and orig_dtype[0] != "u":
@@ -243,13 +232,13 @@ class ImportDICOMDialog(bpy.types.Operator):
         vdb_dirpath.mkdir(parents=True, exist_ok=True)
         vdb_path = Path(vdb_dirpath, f"{uuid4()}.vdb")
 
-        print(f"Storing the VDB file ({vdb_path.as_posix()})...")
-        vdb.write(vdb_path.as_posix(), grids=[grid])
+        print(f"Storing the VDB file ({str(vdb_path)})...")
+        vdb.write(str(vdb_path), grids=[grid])
 
         # Read VDB
         print(f"Importing the VDB file to Blender scene...")
         bpy.ops.object.volume_import(
-            filepath=vdb_path.as_posix(), align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
+            filepath=str(vdb_path), align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
 
         bioxels_obj = bpy.context.active_object
 
@@ -274,7 +263,6 @@ class ImportDICOMDialog(bpy.types.Operator):
         )
 
         bioxels_obj.matrix_world = mat_ras2blender @ mat_scene_scale
-
         bioxels_obj.lock_location[0] = True
         bioxels_obj.lock_location[1] = True
         bioxels_obj.lock_location[2] = True
@@ -297,10 +285,8 @@ class ImportDICOMDialog(bpy.types.Operator):
         container_obj = bpy.context.active_object
         bbox_verts = calc_bbox_verts((0, 0, 0), bioxels_shape)
         for index, vert in enumerate(container_obj.data.vertices):
-            co = transfrom @ mathutils.Vector(bbox_verts[index])
-            co = mat_ras2blender @ co
-            co = mat_scene_scale @ co
-            vert.co = co
+            bbox_transform = mat_ras2blender @ mat_scene_scale @ transfrom
+            vert.co = bbox_transform @ mathutils.Vector(bbox_verts[index])
 
         bioxels_obj.parent = container_obj
         container_obj.name = name
@@ -333,10 +319,11 @@ class ImportDICOMDialog(bpy.types.Operator):
             nodes = node_tree.nodes
             links = node_tree.links
 
-            input_node = nodes.get("Group Input")
-            output_node = nodes.get("Group Output")
-            segment_node = custom_nodes.add_node(nodes, 'BioxelNodes_Segment')
+            input_node = get_node_by_type(nodes, 'NodeGroupInput')[0]
+            output_node = get_node_by_type(nodes, 'NodeGroupOutput')[0]
 
+            segment_node = custom_nodes.add_node(
+                nodes, 'BioxelNodes_Segment')
             links.new(input_node.outputs[0], segment_node.inputs[0])
             links.new(segment_node.outputs[0], output_node.inputs[0])
 
@@ -360,8 +347,8 @@ class ImportDICOMDialog(bpy.types.Operator):
 
 class ReadDICOM(bpy.types.Operator):
     bl_idname = "bioxelnodes.read_dicom"
-    bl_label = "Volume Data as Biovels"
-    bl_description = "Import Volume Data as Biovels (VDB)."
+    bl_label = "Volume Data as Bioxels"
+    bl_description = "Import Volume Data as Bioxels (VDB)."
     bl_options = {'UNDO'}
 
     filepath: bpy.props.StringProperty(
@@ -373,9 +360,14 @@ class ReadDICOM(bpy.types.Operator):
     )  # type: ignore
 
     def execute(self, context):
+        if Path(self.filepath).suffix not in SUPPORT_EXTS:
+            self.report({"WARNING"}, "Not Supported extension.")
+            return {'CANCELLED'}
+
         files = get_data_files(self.filepath)
 
         import SimpleITK as sitk
+
         image = sitk.ReadImage(files)
 
         print("Collecting Meta Data...")
@@ -403,9 +395,6 @@ class ReadDICOM(bpy.types.Operator):
         if not self.filepath:
             return {'CANCELLED'}
 
-        if Path(self.filepath).suffix not in SUPPORT_EXTS:
-            return {'CANCELLED'}
-
         show_message('Reading image data, it may take a while',
                      'Please be patient...')
         context.window_manager.modal_handler_add(self)
@@ -414,8 +403,8 @@ class ReadDICOM(bpy.types.Operator):
 
 class ImportDICOM(bpy.types.Operator):
     bl_idname = "bioxelnodes.import_dicom"
-    bl_label = "Volume Data as Biovels"
-    bl_description = "Import Volume Data as Biovels (VDB)."
+    bl_label = "Volume Data as Bioxels"
+    bl_description = "Import Volume Data as Bioxels (VDB)."
     bl_options = {'UNDO'}
 
     filepath: bpy.props.StringProperty(
@@ -457,18 +446,18 @@ class ExportVDB(bpy.types.Operator):
 
     filename_ext = ".vdb"
 
-    def invoke(self, context, event):
+    @classmethod
+    def poll(cls, context):
         bioxels_obj = None
         for obj in bpy.context.selected_objects:
             bioxels_obj = get_bioxels_obj(obj)
             break
 
-        if bioxels_obj:
-            context.window_manager.fileselect_add(self)
-            return {'RUNNING_MODAL'}
-        else:
-            self.report({"WARNING"}, "Cannot find any bioxels.")
-            return {'CANCELLED'}
+        return True if bioxels_obj else False
+
+    def invoke(self, context, event):
+        context.window_manager.fileselect_add(self)
+        return {'RUNNING_MODAL'}
 
     def execute(self, context):
         bioxels_obj = None
@@ -477,10 +466,15 @@ class ExportVDB(bpy.types.Operator):
             break
 
         filepath = f"{self.filepath.split('.')[0]}.vdb"
+        # "//"
+        source_dir = bpy.path.abspath(bioxels_obj.data.filepath)
+
         output_path: Path = Path(filepath).resolve()
-        source_path: Path = Path(bioxels_obj.data.filepath).resolve()
+        source_path: Path = Path(source_dir).resolve()
         # print('output_path', output_path)
         # print('source_path', source_path)
         shutil.copy(source_path, output_path)
 
+        self.report({"INFO"}, f"Successfully exported to {output_path}")
+
         return {'FINISHED'}

bioxelnodes/menu.py

@@ -1,8 +1,20 @@
+from bioxelnodes.misc import SaveBioxels
 import bpy
 from .convert import ConvertToMesh
 from .io import ExportVDB, ImportDICOM
 
 
+class ObjectMenu(bpy.types.Menu):
+    bl_idname = "BIOXELNODES_MT_OBJECT"
+    bl_label = "Bioxels"
+
+    def draw(self, context):
+        layout = self.layout
+        layout.operator(SaveBioxels.bl_idname)
+        layout.separator()
+        layout.operator(ConvertToMesh.bl_idname)
+
+
 def TOPBAR_FILE_IMPORT(self, context):
     layout = self.layout
     layout.separator()
@@ -17,7 +29,8 @@ def TOPBAR_FILE_EXPORT(self, context):
 
 def VIEW3D_OBJECT(self, context):
     layout = self.layout
-    layout.operator(ConvertToMesh.bl_idname)
+    layout.menu(ObjectMenu.bl_idname)
+
     layout.separator()
 
 

bioxelnodes/misc.py

@@ -0,0 +1,103 @@
+from pathlib import Path
+import shutil
+from bioxelnodes.utils import get_all_bioxels_objs, get_bioxels_obj
+import bpy
+
+
+class SaveBioxels(bpy.types.Operator):
+    bl_idname = "bioxelnodes.save_bioxels"
+    bl_label = "Save Bioxels"
+    bl_description = "Save Bioxels to Directory."
+    bl_options = {'UNDO'}
+
+    @classmethod
+    def poll(cls, context):
+        bioxels_obj = None
+        for obj in bpy.context.selected_objects:
+            bioxels_obj = get_bioxels_obj(obj)
+            break
+
+        return True if bioxels_obj else False
+
+    def execute(self, context):
+        bioxels_objs = []
+
+        for obj in bpy.context.selected_objects:
+            bioxels_obj = get_bioxels_obj(obj)
+            if bioxels_obj:
+                bioxels_objs.append(bioxels_obj)
+
+        if len(bioxels_objs) == 0:
+            self.report({"WARNING"}, "Cannot find any bioxels.")
+            return {'FINISHED'}
+
+        for bioxels_obj in bioxels_objs:
+            name = bioxels_obj.parent.name
+
+            # "//"
+            bioxels_dir = bpy.path.abspath(context.scene.bioxels_dir)
+            source_dir = bpy.path.abspath(bioxels_obj.data.filepath)
+
+            output_path: Path = Path(bioxels_dir, f"{name}.vdb").resolve()
+            source_path: Path = Path(source_dir).resolve()
+
+            if output_path != source_path:
+                shutil.copy(source_path, output_path)
+
+            blend_path = Path(bpy.path.abspath("//")).resolve()
+            bioxels_obj.data.filepath = bpy.path.relpath(
+                str(output_path), start=str(blend_path))
+
+        self.report({"INFO"}, f"Successfully saved bioxels")
+
+        return {'FINISHED'}
+
+
+class SaveAllBioxels(bpy.types.Operator):
+    bl_idname = "bioxelnodes.save_all_bioxels"
+    bl_label = "Save All Bioxels"
+    bl_description = "Save All Bioxels to Directory."
+    bl_options = {'UNDO'}
+
+    def execute(self, context):
+
+        bioxels_objs = get_all_bioxels_objs()
+
+        if len(bioxels_objs) == 0:
+            self.report({"WARNING"}, "Cannot find any bioxels.")
+            return {'FINISHED'}
+
+        for bioxels_obj in bioxels_objs:
+            name = bioxels_obj.parent.name
+
+            # "//"
+            bioxels_dir = bpy.path.abspath(context.scene.bioxels_dir)
+            source_dir = bpy.path.abspath(bioxels_obj.data.filepath)
+
+            output_path: Path = Path(bioxels_dir, f"{name}.vdb").resolve()
+            source_path: Path = Path(source_dir).resolve()
+
+            if output_path != source_path:
+                shutil.copy(source_path, output_path)
+
+            blend_path = Path(bpy.path.abspath("//")).resolve()
+            bioxels_obj.data.filepath = bpy.path.relpath(
+                str(output_path), start=str(blend_path))
+
+        self.report({"INFO"}, f"Successfully saved bioxels")
+
+        return {'FINISHED'}
+
+
+class BIOXELNODES_PT_Bioxels(bpy.types.Panel):
+    bl_idname = "BIOXELNODES_PT_Bioxels"
+    bl_label = "Bioxels"
+    bl_space_type = "PROPERTIES"
+    bl_region_type = "WINDOW"
+    bl_context = "scene"
+
+    def draw(self, context):
+        layout = self.layout
+        scene = context.scene
+        layout.prop(scene, 'bioxels_dir')
+        layout.operator(SaveAllBioxels.bl_idname)

bioxelnodes/nodes.py

@@ -1,6 +1,6 @@
 
 from pathlib import Path
-from .custom_nodes import CustomNodes
+from .customnodes import CustomNodes
 import bpy
 
 
@@ -9,8 +9,8 @@ def add_driver_to_node_factory(source_prop, target_prop):
 import bpy
 from bioxelnodes.utils import add_direct_driver, get_bioxels_obj
 bioxels_obj = get_bioxels_obj(bpy.context.active_object)
-container_obj = bioxels_obj.parent
 if bioxels_obj:
+    container_obj = bioxels_obj.parent
     add_direct_driver(
         target=node,
         target_prop='{target_prop}',
@@ -28,9 +28,10 @@ def set_prop_to_node_factory(source_prop, target_prop):
 import bpy
 from bioxelnodes.utils import get_bioxels_obj
 bioxels_obj = get_bioxels_obj(bpy.context.active_object)
-container_obj = bioxels_obj.parent
 if bioxels_obj:
-    node.inputs.get('{target_prop}').default_value = container_obj.get('{source_prop}')
+    container_obj = bioxels_obj.parent
+    node.inputs.get('{target_prop}').default_value = container_obj.get(
+        '{source_prop}')
 else:
     print('Cannot find any bioxels.')
     """
@@ -44,7 +45,7 @@ MENU_ITEMS = [
         'items': [
             {
                 'label': 'Segment',
-                'icon': 'OUTLINER_OB_META',
+                'icon': 'BONE_DATA',
                 'node_type': 'BioxelNodes_Segment',
                 'node_description': '',
                 'node_callback': "\n".join([
@@ -54,7 +55,7 @@ MENU_ITEMS = [
             },
             {
                 'label': 'Anatomy',
-                'icon': 'OUTLINER_OB_META',
+                'icon': 'CONSTRAINT_BONE',
                 'node_type': 'BioxelNodes_Anatomy',
                 'node_description': '',
                 'node_callback': "\n".join([
@@ -140,7 +141,7 @@ MENU_ITEMS = [
 
 custom_nodes = CustomNodes(
     menu_items=MENU_ITEMS,
-    nodes_file=Path(__file__).parent/"assets/Nodes.blend",
-    root_label='BioxelNodes',
+    nodes_file=Path(__file__).parent/"assets/Nodes/BioxelNodes.blend",
+    root_label='Bioxel Nodes',
     root_icon="FILE_VOLUME",
 )

bioxelnodes/preferences.py

@@ -1,23 +1,22 @@
 import bpy
 from pathlib import Path
-from .external_package import ExternalPackagePreferences
+from .externalpackage import ExternalPackagePreferences
 
 
 class BioxelNodesPreferences(bpy.types.AddonPreferences, ExternalPackagePreferences):
     bl_idname = __package__
 
     cache_dir: bpy.props.StringProperty(
-        name="Python Log Directory",
+        name="VDB Cache Directory",
         subtype='DIR_PATH',
-        default=Path(Path.home(), '.bioxelnodes').as_posix()
+        default=str(Path(Path.home(), '.bioxelnodes'))
     )  # type: ignore
 
-
     def draw(self, context):
         layout = self.layout
         layout.label(text="Configuration")
         layout.prop(self, 'cache_dir', text='Set Cache Directory')
 
         # ExternalPackagePreferences Config
-        self.requirements_dir = Path(__file__).parent.as_posix()
+        self.requirements_dir = str(Path(__file__).parent)
         super().draw(context)

bioxelnodes/utils.py

@@ -2,6 +2,10 @@ import bpy
 import mathutils
 
 
+def get_node_by_type(nodes, type_name: str):
+    return [node for node in nodes if type(node).__name__ == type_name]
+
+
 def show_message(message="", title="Message Box", icon='INFO'):
 
     def draw(self, context):
@@ -77,6 +81,15 @@ def get_bioxels_obj(current_obj):
 
     return bioxels_obj
 
+def get_all_bioxels_objs():
+    bioxels_objs = []
+
+    for obj in bpy.data.objects:
+        if obj.parent:
+            if obj.parent.get('bioxels_container') and obj.get('bioxels'):
+                bioxels_objs.append(obj)
+    
+    return list(set(bioxels_objs))
 
 def extract_last_number(text):
     # Initialize an empty string to store the digits