Merge pull request #12 from OmooLab/feature/dev

Feature/dev

.prettierrc

@@ -0,0 +1,11 @@
+{
+  "tabWidth": 2,
+  "overrides": [
+    {
+      "files": "*.md",
+      "options": {
+        "tabWidth": 4
+      }
+    }
+  ]
+}

README.md

@@ -15,96 +15,31 @@ Before us, there have been many tutorials and add-ons for importing volumetric d
 
 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)
+![gallery](assets/gallery.png)
+
+The "Bioxel" in "BioxelNodes", is a combination of the words "Bio-" and "Voxel". Bioxel is a voxel that stores biological data. 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. [Getting Started](https://omoolab.github.io/BioxelNodes/latest/getting-started)
+
+# Supported Format
+
+| Format | EXT                                      | Test    |
+| ------ | ---------------------------------------- | ------- |
+| DICOM  | .dcm, .DICOM                             | ✅ pass |
+| BMP    | .bmp, .BMP                               | ✅ pass |
+| JPEG   | .jpg, .JPG, .jpeg, .JPEG                 | ✅ pass |
+| PNG    | .png, .PNG                               | ✅ pass |
+| TIFF   | .tif, .TIF, .tiff, .TIFF                 | ✅ pass |
+| Nifti  | .nia, .nii, .nii.gz, .hdr, .img, .img.gz | ✅ pass |
+| Nrrd   | .nrrd, .nhdr                             | ✅ pass |
+| Meta   | .mha, .mhd                               | yet     |
+| HDF5   | .hdf, .h4, .hdf4, .he2, .h5, .hdf5, .he5 | ✅ pass |
+| VTK    | .vtk                                     | yet     |
+| BioRad | .PIC, .pic                               | yet     |
+| Gipl   | .gipl, .gipl.gz                          | yet     |
+| LSM    | .lsm, .LSM                               | yet     |
+| MINC   | .mnc, .MNC                               | yet     |
+| MRC    | .mrc, .rec                               | yet     |
+
+# Known limitations
 
-### 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.
+- Time sequence volume not supported (will be supported soon)

bioxelnodes/__init__.py

@@ -1,40 +1,33 @@
-from .nodes import custom_nodes
-from . import auto_load
-from . import menu
-
 import bpy
 
+from . import auto_load
+from . import menus
+
 
 bl_info = {
     "name": "Bioxel Nodes",
     "author": "Ma Nan",
     "description": "",
-    "blender": (4, 1, 0),
-    "version": (0, 1, 0),
+    "blender": (4, 0, 0),
+    "version": (0, 1, 1),
     "location": "File -> Import",
     "warning": "",
     "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()
-    custom_nodes.register()
-    menu.create_menu()
+    menus.add()
+    bpy.types.Scene.bioxels_dir = bpy.props.StringProperty(
+        name="Bioxels Directory",
+        subtype='DIR_PATH',
+        default="//"
+    )
 
 
 def unregister():
-    try:
-        menu.remove_menu()
-        custom_nodes.unregister()
-        auto_load.unregister()
-    except RuntimeError:
-        pass
+    menus.remove()
+    auto_load.unregister()

bioxelnodes/auto_load.py

@@ -16,13 +16,15 @@
 modules = None
 ordered_classes = None
 
+
 def init():
     global modules
     global ordered_classes
 
     modules = get_all_submodules(Path(__file__).parent)
     ordered_classes = get_ordered_classes_to_register(modules)
 
+
 def register():
     for cls in ordered_classes:
         bpy.utils.register_class(cls)
@@ -33,15 +35,22 @@ def register():
         if hasattr(module, "register"):
             module.register()
 
+
 def unregister():
     for cls in reversed(ordered_classes):
-        bpy.utils.unregister_class(cls)
+        try:
+            bpy.utils.unregister_class(cls)
+        except Exception as e:
+            print(f"Fail to unregister {cls}, skiped")
 
     for module in modules:
-        if module.__name__ == __name__:
-            continue
-        if hasattr(module, "unregister"):
-            module.unregister()
+        try:
+            if module.__name__ == __name__:
+                continue
+            if hasattr(module, "unregister"):
+                module.unregister()
+        except Exception as e:
+            print(f"Fail to unregister {module}, skiped")
 
 
 # Import modules
@@ -50,10 +59,12 @@ def unregister():
 def get_all_submodules(directory):
     return list(iter_submodules(directory, directory.name))
 
+
 def iter_submodules(path, package_name):
     for name in sorted(iter_submodule_names(path)):
         yield importlib.import_module("." + name, package_name)
 
+
 def iter_submodule_names(path, root=""):
     for _, module_name, is_package in pkgutil.iter_modules([str(path)]):
         if is_package:
@@ -70,26 +81,32 @@ def iter_submodule_names(path, root=""):
 def get_ordered_classes_to_register(modules):
     return toposort(get_register_deps_dict(modules))
 
+
 def get_register_deps_dict(modules):
     my_classes = set(iter_my_classes(modules))
-    my_classes_by_idname = {cls.bl_idname : cls for cls in my_classes if hasattr(cls, "bl_idname")}
+    my_classes_by_idname = {
+        cls.bl_idname: cls for cls in my_classes if hasattr(cls, "bl_idname")}
 
     deps_dict = {}
     for cls in my_classes:
-        deps_dict[cls] = set(iter_my_register_deps(cls, my_classes, my_classes_by_idname))
+        deps_dict[cls] = set(iter_my_register_deps(
+            cls, my_classes, my_classes_by_idname))
     return deps_dict
 
+
 def iter_my_register_deps(cls, my_classes, my_classes_by_idname):
     yield from iter_my_deps_from_annotations(cls, my_classes)
     yield from iter_my_deps_from_parent_id(cls, my_classes_by_idname)
 
+
 def iter_my_deps_from_annotations(cls, my_classes):
     for value in typing.get_type_hints(cls, {}, {}).values():
         dependency = get_dependency_from_annotation(value)
         if dependency is not None:
             if dependency in my_classes:
                 yield dependency
 
+
 def get_dependency_from_annotation(value):
     if blender_version >= (2, 93):
         if isinstance(value, bpy.props._PropertyDeferred):
@@ -100,6 +117,7 @@ def get_dependency_from_annotation(value):
                 return value[1]["type"]
     return None
 
+
 def iter_my_deps_from_parent_id(cls, my_classes_by_idname):
     if bpy.types.Panel in cls.__bases__:
         parent_idname = getattr(cls, "bl_parent_id", None)
@@ -108,33 +126,37 @@ def iter_my_deps_from_parent_id(cls, my_classes_by_idname):
             if parent_cls is not None:
                 yield parent_cls
 
+
 def iter_my_classes(modules):
     base_types = get_register_base_types()
     for cls in get_classes_in_modules(modules):
         if any(base in base_types for base in cls.__bases__):
             if not getattr(cls, "is_registered", False):
                 yield cls
 
+
 def get_classes_in_modules(modules):
     classes = set()
     for module in modules:
         for cls in iter_classes_in_module(module):
             classes.add(cls)
     return classes
 
+
 def iter_classes_in_module(module):
     for value in module.__dict__.values():
         if inspect.isclass(value):
             yield value
 
+
 def get_register_base_types():
     return set(getattr(bpy.types, name) for name in [
         "Panel", "Operator", "PropertyGroup", "FileHandler",
         "AddonPreferences", "Header", "Menu",
         "Node", "NodeSocket", "NodeTree",
         "UIList", "RenderEngine",
         "Gizmo", "GizmoGroup",
-    ])
+    ] if hasattr(bpy.types, name))
 
 
 # Find order to register to solve dependencies
@@ -151,5 +173,6 @@ def toposort(deps_dict):
                 sorted_values.add(value)
             else:
                 unsorted.append(value)
-        deps_dict = {value : deps_dict[value] - sorted_values for value in unsorted}
+        deps_dict = {value: deps_dict[value] -
+                     sorted_values for value in unsorted}
     return sorted_list

bioxelnodes/convert.py

@@ -5,7 +5,7 @@
 class ConvertToMesh(bpy.types.Operator):
     bl_idname = "bioxelnodes.convert_to_mesh"
     bl_label = "Bioxels To Mesh"
-    bl_description = "Convert Bioxels To Mesh."
+    bl_description = "Convert Bioxels To Mesh"
     bl_options = {'UNDO'}
 
     @classmethod

bioxelnodes/customnodes/__init__.py

@@ -1 +1 @@
-from .menu import CustomNodes
+from .menus import CustomNodes

bioxelnodes/customnodes/menu.py → bioxelnodes/customnodes/menus.py

@@ -3,12 +3,6 @@
 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"
@@ -182,12 +176,17 @@ def register(self):
             bpy.utils.register_class(cls)
 
         bpy.types.NODE_MT_add.append(self.add_node_menu)
+        bpy.types.Scene.custom_nodes_dir = bpy.props.StringProperty(
+            name="Nodes Directory",
+            subtype='DIR_PATH',
+            default="//"
+        )
 
     def unregister(self):
+        bpy.types.NODE_MT_add.remove(self.add_node_menu)
         try:
             for cls in reversed(self.menu_classes):
                 bpy.utils.unregister_class(cls)
 
-            bpy.types.NODE_MT_add.remove(self.add_node_menu)
         except RuntimeError:
             pass

bioxelnodes/externalpackage/__init__.py

@@ -1 +1,2 @@
-from .preferences import ExternalPackagePreferences
+from .preferences import ExternalPackagePreferences
+from .package import PackageInstaller