Feature/dev

.github/workflows/upload-assets.yml

@@ -22,7 +22,7 @@ jobs:
   #       id: draft_release
   #       uses: cardinalby/[email protected]
   #       with:
-  #         releaseName: Draft
+  #         releaseName: Upload
   #       env:
   #         GITHUB_TOKEN: ${{ github.token }}
 
@@ -70,5 +70,38 @@ jobs:
         with:
           upload_url: ${{ needs.draft_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps
           asset_path: ./package.zip
-          asset_name: BioxelNodes_${{ needs.draft_release.outputs.version }}.zip
+          asset_name: BioxelNodes_Addon_${{ needs.draft_release.outputs.version }}.zip
+          asset_content_type: application/zip
+
+  upload_blender_extension:
+    name: Upload Blender Extension
+    needs: draft_release
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v4
+        with:
+          lfs: 'true'
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+      - name: Zip Extension
+        run: |
+          pip download SimpleITK --dest bioxelnodes/wheels --only-binary=:all: --python-version=3.11 --platform=macosx_11_0_arm64
+          pip download SimpleITK --dest bioxelnodes/wheels --only-binary=:all: --python-version=3.11 --platform=win_amd64
+          rm -r bioxelnodes/externalpackage
+          cp extension/__init__.py bioxelnodes/__init__.py
+          cp extension/preferences.py bioxelnodes/preferences.py
+          cp extension/blender_manifest.toml bioxelnodes/blender_manifest.toml
+          zip -r package.zip bioxelnodes
+      - name: Upload Release Asset
+        id: upload-release-asset
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          upload_url: ${{ needs.draft_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps
+          asset_path: ./package.zip
+          asset_name: BioxelNodes_Extension_${{ needs.draft_release.outputs.version }}.zip
           asset_content_type: application/zip

README.md

@@ -15,7 +15,7 @@ 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/assets/gallery.png)
+![cover](docs/assets/cover.png)
 
 The "Bioxel" in "Bioxel Nodes", is a combination of the words "Bio-" and "Voxel". Bioxel is a voxel that stores biological data. We are developing a toolkit around Bioxel 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)
 

bioxelnodes/auto_load.py

@@ -57,7 +57,7 @@ def unregister():
 #################################################
 
 def get_all_submodules(directory):
-    return list(iter_submodules(directory, directory.name))
+    return list(iter_submodules(directory, __package__))
 
 
 def iter_submodules(path, package_name):

bioxelnodes/externalpackage/package.py

@@ -76,7 +76,8 @@ def start_logging(self, logfile_name: str = 'side-packages-install') -> logging.
 
         # Set up logging configuration
         logfile_path = Path(self.log_path, f"{logfile_name}.log")
-        logging.basicConfig(filename=logfile_path, level=logging.INFO)
+        logging.basicConfig(filename=logfile_path,
+                            level=logging.INFO, encoding='utf-8')
 
         # Return logger object
         return logging.getLogger()
@@ -248,13 +249,16 @@ def run_python(self, cmd_list: list = None, timeout: int = 600):
         result = subprocess.run(cmd_list, timeout=timeout,
                                 stdout=subprocess.PIPE, stderr=subprocess.PIPE)
 
-        if result.returncode != 0:
-            log.error('Command failed: %s', cmd_list)
-            log.error('stdout: %s', result.stdout.decode())
-            log.error('stderr: %s', result.stderr.decode(errors='ignore'))
-        else:
-            log.info('Command succeeded: %s', cmd_list)
-            log.info('stdout: %s', result.stdout.decode())
+        try:
+            if result.returncode != 0:
+                log.error('Command failed: %s', cmd_list)
+                log.error('stdout: %s', result.stdout.decode())
+                log.error('stderr: %s', result.stderr.decode(errors='ignore'))
+            else:
+                log.info('Command succeeded: %s', cmd_list)
+                log.info('stdout: %s', result.stdout.decode())
+        except:
+            ...
         # return the command list, return code, stdout, and stderr as a tuple
         return result
 

bioxelnodes/io_points.py

@@ -22,200 +22,4 @@ def create_points_obj(points, name="points"):
     # make the bmesh the object's mesh
     bm.to_mesh(mesh)
     bm.free()  # always do this when finished
-    return obj
-
-
-# class ImportDICOMPointsDialog(bpy.types.Operator):
-#     bl_idname = "bioxelnodes.import_dicom_points_dialog"
-#     bl_label = "Volume Data as Bioxels"
-#     bl_description = "Import Volume Data as Bioxels (VDB)"
-#     bl_options = {'UNDO'}
-
-#     filepath: bpy.props.StringProperty(
-#         subtype="FILE_PATH",
-#         options={'HIDDEN'}
-#     )  # type: ignore
-
-#     bioxels_shape: bpy.props.IntVectorProperty(
-#         name="Bioxels Shape (ReadOnly)",
-#         min=0,
-#         default=(100, 100, 100)
-#     )  # type: ignore
-
-#     bioxel_size: bpy.props.FloatProperty(
-#         name="Bioxel Size",
-#         soft_min=0.1, soft_max=10.0,
-#         min=1e-2, max=1e2,
-#         default=1,
-#         update=on_bioxel_size_changed
-#     )  # type: ignore
-
-#     orig_spacing: bpy.props.FloatVectorProperty(
-#         name="Original Spacing",
-#         default=(1, 1, 1),
-#         update=on_orig_spacing_changed
-#     )  # type: ignore
-
-#     orig_shape: bpy.props.IntVectorProperty(
-#         name="Original Shape",
-#         default=(100, 100, 100),
-#         options={'HIDDEN'}
-#     )  # type: ignore
-
-#     auto: bpy.props.BoolProperty(
-#         name="Auto Setting",
-#         default=False,
-#         options={'HIDDEN'}
-#     )  # type: ignore
-
-#     scene_scale: bpy.props.FloatProperty(
-#         name="Scene Scale",
-#         soft_min=0.001, soft_max=100.0,
-#         min=1e-6, max=1e6,
-#         default=0.01,
-#     )  # type: ignore
-
-#     do_add_segmentnode: bpy.props.BoolProperty(
-#         name="Add Segment Node",
-#         default=True,
-#     )  # type: ignore
-
-#     do_change_render_setting: bpy.props.BoolProperty(
-#         name="Change Render Setting",
-#         default=True,
-#     )  # type: ignore
-
-#     def execute(self, context):
-#         files = get_data_files(self.filepath)
-#         name = Path(self.filepath).parent.name
-
-#         image = sitk.ReadImage(files)
-
-#         bioxel_size = float(self.bioxel_size)
-#         orig_spacing = tuple(self.orig_spacing)
-#         image_spacing = image.GetSpacing()
-#         image_shape = image.GetSize()
-
-#         bioxels_spacing = (
-#             image_spacing[0] / orig_spacing[0] * bioxel_size,
-#             image_spacing[1] / orig_spacing[1] * bioxel_size,
-#             image_spacing[2] / orig_spacing[2] * bioxel_size
-#         )
-
-#         bioxels_shape = (
-#             int(image_shape[0] / bioxel_size * orig_spacing[0]),
-#             int(image_shape[1] / bioxel_size * orig_spacing[1]),
-#             int(image_shape[2] / bioxel_size * orig_spacing[2]),
-#         )
-
-#         print("Resampling...")
-#         image = sitk.Resample(
-#             image1=image,
-#             size=bioxels_shape,
-#             transform=sitk.Transform(),
-#             interpolator=sitk.sitkLinear,
-#             outputOrigin=image.GetOrigin(),
-#             outputSpacing=bioxels_spacing,
-#             outputDirection=image.GetDirection(),
-#             defaultPixelValue=0,
-#             outputPixelType=image.GetPixelID(),
-#         )
-
-#         print("Orienting to RAS...")
-#         image = sitk.DICOMOrient(image, 'RAS')
-
-#         array = sitk.GetArrayFromImage(image)
-#         orig_dtype = str(array.dtype)
-#         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]
-#         # https://www.slicer.org/wiki/Coordinate_systems
-
-#         # ITK                  Numpy      3D
-#         # R (ight)     i   ->    k   ->   x
-#         # A (nterior)  j   ->    j   ->   y
-#         # S (uperior)  k   ->    i   ->   z
-
-#         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":
-#             bioxels_offset = -bioxels_min
-#             array = array + np.full_like(array, bioxels_offset)
-#             bioxels_max = float(np.max(array))
-#             bioxels_min = float(np.min(array))
-#             print("Offseted Max:", bioxels_max)
-#             print("Offseted Min:", bioxels_min)
-
-#         points = []
-#         for x in range(array.shape[0]):
-#             for y in range(array.shape[1]):
-#                 for z in range(array.shape[2]):
-#                     points.append({
-#                         "pos": (x, y, z),
-#                         "value": array[x, y, z],
-#                     })
-
-#         # # Build VDB
-#         # grid = vdb.FloatGrid()
-#         # grid.copyFromArray(array.copy())
-
-#         # # After sitk.DICOMOrient(), origin and direction will also orient base on LPS
-#         # # so we need to convert them into RAS
-#         # mat_lps2ras = axis_conversion(
-#         #     from_forward='-Z',
-#         #     from_up='-Y',
-#         #     to_forward='-Z',
-#         #     to_up='Y'
-#         # ).to_4x4()
-
-#         # mat_location = mathutils.Matrix.Translation(
-#         #     mathutils.Vector(image.GetOrigin())
-#         # )
-
-#         # mat_rotation = mathutils.Matrix(
-#         #     np.array(image.GetDirection()).reshape((3, 3))
-#         # ).to_4x4()
-
-#         # mat_scale = mathutils.Matrix.Scale(
-#         #     bioxel_size, 4
-#         # )
-
-#         # transfrom = mat_lps2ras @ mat_location @ mat_rotation @ mat_scale
-
-#         obj = create_points_obj(points)
-
-#         # Make transformation
-#         scene_scale = float(self.scene_scale)
-#         # (S)uperior  -Z -> Y
-#         # (A)osterior  Y -> Z
-#         mat_ras2blender = axis_conversion(
-#             from_forward='-Z',
-#             from_up='Y',
-#             to_forward='Y',
-#             to_up='Z'
-#         ).to_4x4()
-
-#         mat_scene_scale = mathutils.Matrix.Scale(
-#             scene_scale, 4
-#         )
-
-#         obj.matrix_world = mat_ras2blender @ mat_scene_scale
-
-#         self.report({"INFO"}, "Successfully Imported")
-
-#         return {'FINISHED'}
-
-#     def invoke(self, context, event):
-#         # print(tuple(self.orig_shape))
-#         self.auto = True
-#         self.bioxel_size = 1
-#         context.window_manager.invoke_props_dialog(self)
-#         return {'RUNNING_MODAL'}
+    return obj

bioxelnodes/misc.py

@@ -1,7 +1,7 @@
 import bpy
 from pathlib import Path
 import shutil
-from bioxelnodes.utils import get_all_layers, get_container, get_container_layers
+from .utils import get_all_layers, get_container, get_container_layers
 
 
 def save_layer(layer, output_dir):

bioxelnodes/nodes.py

@@ -7,7 +7,7 @@
 def add_driver_to_node_factory(source_prop, target_prop):
     callback_str = f"""
 import bpy
-from bioxelnodes.utils import add_direct_driver, get_bioxels_obj
+from .utils import add_direct_driver, get_bioxels_obj
 bioxels_obj = get_bioxels_obj(bpy.context.active_object)
 if bioxels_obj:
     container_obj = bioxels_obj.parent
@@ -26,7 +26,7 @@ def add_driver_to_node_factory(source_prop, target_prop):
 def set_prop_to_node_factory(source_prop, target_prop):
     callback_str = f"""
 import bpy
-from bioxelnodes.utils import get_bioxels_obj
+from .utils import get_bioxels_obj
 bioxels_obj = get_bioxels_obj(bpy.context.active_object)
 if bioxels_obj:
     container_obj = bioxels_obj.parent

bioxelnodes/preferences.py

@@ -26,5 +26,4 @@ def draw(self, context):
 
         layout.label(text="Configuration")
         layout.prop(self, 'cache_dir')
-
         layout.prop(self, "do_change_render_setting")

docs/getting-started.md

@@ -4,8 +4,19 @@ Currently only support Blender 4.0 or above, make sure you have the correct vers
 
 ## 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.
+#### For Blender 4.2 or higher
+
+Download the **Extension** version `BioxelNodes_Extension_{version}.zip` from https://github.com/OmooLab/BioxelNodes/releases/latest  
+In Blender, Edit > Preferences > Extensions > Install from Disk, select the zip file you just downloaded.
+
+Thats it!
+
+> If it cannot be enable, just reboot blender.
+
+#### For Blender 4.0 or 4.1
+
+Download the **Addon** version `BioxelNodes_Addon_{version}.zip` from https://github.com/OmooLab/BioxelNodes/releases/latest  
+In Blender, Edit > Preferences > Add-ons > Install, select the zip file you just downloaded.
 
 The add-on requires a third-party python dependency called SimpleITK, click `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 that, click `Reboot Blender` button.
 

docs/index.md

@@ -13,7 +13,7 @@ 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](assets/gallery.png)
+![cover](assets/cover.png)
 
 The "Bioxel" in "Bioxel Nodes", is a combination of the words "Bio-" and "Voxel". Bioxel is a voxel that stores biological data. We are developing a toolkit around Bioxel 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)
 

extension/__init__.py

@@ -0,0 +1,22 @@
+import bpy
+
+from . import auto_load
+from . import menus
+
+
+auto_load.init()
+
+
+def register():
+    auto_load.register()
+    menus.add()
+    bpy.types.Scene.bioxel_layer_dir = bpy.props.StringProperty(
+        name="Bioxel Layers Directory",
+        subtype='DIR_PATH',
+        default="//"
+    )
+
+
+def unregister():
+    menus.remove()
+    auto_load.unregister()