Merge pull request #38 from OmooLab/fix-import

fix: color ramp not fit

.github/workflows/build-addon.yml

@@ -50,33 +50,13 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
-  upload_blender_addon:
+  build_blender_add-on:
-    name: Upload Blender Add-on
+    name: Build Blender Extension
-    needs: draft_release
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout Code
-        uses: actions/checkout@v4
-        with:
-          lfs: "true"
-      - name: Zip Add-on
-        run: |
-          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: ${{ needs.draft_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps
-          asset_path: ./package.zip
-          asset_name: BioxelNodes_Addon_${{ 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
+    strategy:
+      matrix:
+        platform: ["windows-x64", "linux-x64", "macos-arm64", "macos-x64"]
     steps:
       - name: Checkout Code
         uses: actions/checkout@v4
@@ -86,13 +66,10 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: 3.11
-      - name: Zip Extension
+      - name: Build Add-on
         run: |
-          pip download SimpleITK==2.3.1 --dest bioxelnodes/wheels --only-binary=:all: --python-version=3.11 --platform=win_amd64
+          pip install tomlkit
-          rm -r bioxelnodes/externalpackage
+          python build.py ${{ matrix.platform }}
-          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
@@ -102,5 +79,5 @@ jobs:
         with:
           upload_url: ${{ needs.draft_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps
           asset_path: ./package.zip
-          asset_name: BioxelNodes_Extension_${{ needs.draft_release.outputs.version }}.zip
+          asset_name: BioxelNodes_${{ needs.draft_release.outputs.version }}_${{ matrix.platform }}.zip
           asset_content_type: application/zip

.gitignore

@@ -133,4 +133,4 @@ blendcache_*
 
 .secrets
 
-!bioxelnodes/scipy/_nd_image.cp311-win_amd64.pyd
+!scipy_ndimage/*/**

README.md

@@ -2,29 +2,33 @@
 
 # Bioxel Nodes
 
-![Static Badge](https://img.shields.io/badge/Blender-orange?style=for-the-badge&logo=blender&logoColor=white)
+[![For Blender](https://img.shields.io/badge/Blender-orange?style=for-the-badge&logo=blender&logoColor=white&color=black)](https://blender.org/)
-![GitHub License](https://img.shields.io/github/license/OmooLab/BioxelNodes?style=for-the-badge)
+![GitHub License](https://img.shields.io/github/license/OmooLab/BioxelNodes?style=for-the-badge&labelColor=black)
-![GitHub Release](https://img.shields.io/github/v/release/OmooLab/BioxelNodes?style=for-the-badge)
+![GitHub Release](https://img.shields.io/github/v/release/OmooLab/BioxelNodes?style=for-the-badge&labelColor=black)
-![GitHub Repo stars](https://img.shields.io/github/stars/OmooLab/BioxelNodes?style=for-the-badge)
+![GitHub Repo stars](https://img.shields.io/github/stars/OmooLab/BioxelNodes?style=for-the-badge&labelColor=black)
+
+[![Discord](https://img.shields.io/discord/1265129134397587457?style=for-the-badge&logo=discord&label=Discord&labelColor=white&color=black)](https://discord.gg/pYkNyq2TjE)
 
 Bioxel Nodes is a Blender addon for scientific volumetric data visualization. It using Blender's powerful **Geometry Nodes** and **Cycles** to process and render volumetric data.
 
 ![cover](https://omoolab.github.io/BioxelNodes/latest/assets/cover.png)
 
--   Fantastic rendering result, also support EEVEE NEXT
+-   Realistic rendering result, also support EEVEE NEXT.
--   Support multiple formats
+-   Support multiple formats.
--   Support 4D volumetric data
+-   Support 4D volumetric data.
--   All kinds of cutters
+-   All kinds of cutters.
--   Simple and powerful nodes
+-   Simple and powerful nodes.
 -   Based on blender natively, can work without addon.
 
-**Click [Getting Started](https://omoolab.github.io/BioxelNodes/latest/installation) to begin your journey into visualizing volumetric data!**
+**Read the [getting started](https://omoolab.github.io/BioxelNodes/latest/installation) to begin your journey into visualizing volumetric data!**
+
+Welcome to our [discord server](https://discord.gg/pYkNyq2TjE), if you have any problems with this add-on.
 
 ## Support Multiple Formats
 
 | Format | EXT                                      | Test    |
 | ------ | ---------------------------------------- | ------- |
-| DICOM  | .dcm, .DICOM                             | ✅ pass |
+| DICOM  | .dcm, .DCM, .DICOM, .ima, .IMA           | ✅ pass |
 | BMP    | .bmp, .BMP                               | ✅ pass |
 | JPEG   | .jpg, .JPG, .jpeg, .JPEG                 | ✅ pass |
 | PNG    | .png, .PNG                               | ✅ pass |
@@ -32,6 +36,8 @@ Bioxel Nodes is a Blender addon for scientific volumetric data visualization. It
 | Nifti  | .nia, .nii, .nii.gz, .hdr, .img, .img.gz | ✅ pass |
 | Nrrd   | .nrrd, .nhdr                             | ✅ pass |
 | HDF5   | .hdf, .h4, .hdf4, .he2, .h5, .hdf5, .he5 | ✅ pass |
+| OME    | .ome.tiff, .ome.tif                      | ✅ pass |
+| MRC    | .mrc, .mrc.gz, .map, .map.gz             | ✅ pass |
 
 ## Support 4D volumetric data
 
@@ -53,15 +59,15 @@ Bioxel Nodes is a Blender addon for scientific volumetric data visualization. It
 -   Only works with Cycles CPU , Cycles GPU (OptiX), EEVEE
 -   Section surface cannot be generated when convert to mesh (will be supported soon)
 
-## Compatibile to Newer Version
+## Compatible to Newer Version
 
-**Updating this addon may break old files, so read the following carefully before updating**
+**v0.3.x is not compatible to v0.2.x, Updating this addon may break old files. Read the following carefully before upgradation**
 
-Before updating this addon, you need to ask yourself whether this project file will be modified again or not, if it's an archived project file, I would recommend that you run **Bioxel Nodes > Save Staged Data** to make the addon nodes permanent. In this way, there will be no potential problem with the nodes not functioning due to the addon update.
+Before upgradation, you need to ask yourself whether this project file will be modified again or not, if it's an archived project file, I would recommend that you run **Bioxel Nodes > Save Staged Data** to make the addon nodes permanent. In this way, there will be no potential problem with the nodes not functioning due to the addon update.
 
 After the addon update, your old project files may not work either, this may be because you had executed **Save Staged Data**. If so, you need to execute **Bioxel Nodes > Relink Nodes to Addon** to relink them to make sure that the addon's new functionality and the addon nodes are synchronized.
 
-Also, unlike the newer versions, the older shaders are not based on OSL, so if you find that you can't render volumes, you need to turn on **Open Shading Language (OSL)** in the Render Settings.
+Also, the older shaders are not based on OSL, so if you find that you can't render volumes, you need to turn on **Open Shading Language (OSL)** in the Render Settings.
 
 ## Roadmap
 

bioxelnodes/__init__.py

@@ -4,22 +4,13 @@ from . import auto_load
 from . import menus
 
 
-bl_info = {
-    "name": "Bioxel Nodes",
-    "author": "Ma Nan",
-    "description": "",
-    "blender": (4, 1, 0),
-    "version": (0, 2, 7),
-    "location": "File -> Import",
-    "warning": "",
-    "category": "Node"
-}
-
 auto_load.init()
 
 
 def register():
     auto_load.register()
+    bpy.types.WindowManager.bioxelnodes_progress_factor = bpy.props.FloatProperty()
+    bpy.types.WindowManager.bioxelnodes_progress_text = bpy.props.StringProperty()
     menus.add()
 
 

bioxelnodes/bioxel/container.py

@@ -0,0 +1,9 @@
+from .layer import Layer
+
+
+class Container():
+    def __init__(self,
+                 name,
+                 layers: list[Layer] = []) -> None:
+        self.name = name
+        self.layers = layers

bioxelnodes/bioxel/io.py

@@ -0,0 +1,43 @@
+from pathlib import Path
+import uuid
+
+
+# 3rd-party
+import h5py
+
+from .container import Container
+from .layer import Layer
+
+
+def load_container(load_file: str):
+    load_path = Path(load_file).resolve()
+    with h5py.File(load_path, 'r') as file:
+        layers = []
+        for key, layer_dset in file['layers'].items():
+            layers.append(Layer(data=layer_dset[:],
+                                name=layer_dset.attrs['name'],
+                                kind=layer_dset.attrs['kind'],
+                                affine=layer_dset.attrs['affine']))
+
+        container = Container(name=file.attrs['name'],
+                              layers=layers)
+
+        return container
+
+
+def save_container(container: Container, save_file: str, overwrite=False):
+    save_path = Path(save_file).resolve()
+    if overwrite:
+        if save_path.is_file():
+            save_path.unlink()
+
+    with h5py.File(save_path, "w") as file:
+        file.attrs['name'] = container.name
+        layer_group = file.create_group("layers")
+        for layer in container.layers:
+            layer_key = uuid.uuid4().hex[:8]
+            layer_dset = layer_group.create_dataset(name=layer_key,
+                                                    data=layer.data)
+            layer_dset.attrs['name'] = layer.name
+            layer_dset.attrs['kind'] = layer.kind
+            layer_dset.attrs['affine'] = layer.affine

bioxelnodes/bioxel/layer.py

@@ -0,0 +1,143 @@
+import copy
+import numpy as np
+
+from . import scipy
+from . import skimage as ski
+from . import scipy as ndi
+
+# 3rd-party
+import transforms3d
+
+# TODO: turn to dataclasses
+
+
+class Layer():
+    def __init__(self,
+                 data: np.ndarray,
+                 name: str,
+                 kind="scalar",
+                 affine=np.identity(4)) -> None:
+        if data.ndim != 5:
+            raise Exception("Data shape order should be TXYZC")
+
+        affine = np.array(affine)
+        if affine.shape != (4, 4):
+            raise Exception("affine shape should be (4,4)")
+
+        self.data = data
+        self.name = name
+        self.kind = kind
+        self.affine = affine
+
+    @property
+    def bioxel_size(self):
+        t, r, z, s = transforms3d.affines.decompose44(self.affine)
+        return z.tolist()
+
+    @property
+    def shape(self):
+        return self.data.shape[1:4]
+
+    @property
+    def dtype(self):
+        return self.data.dtype
+
+    @property
+    def origin(self):
+        t, r, z, s = transforms3d.affines.decompose44(self.affine)
+        return t.tolist()
+
+    @property
+    def euler(self):
+        t, r, z, s = transforms3d.affines.decompose44(self.affine)
+        return list(transforms3d.euler.mat2euler(r))
+
+    @property
+    def min(self):
+        return float(np.min(self.data))
+
+    @property
+    def frame_count(self):
+        return self.data.shape[0]
+
+    @property
+    def channel_count(self):
+        return self.data.shape[-1]
+
+    @property
+    def max(self):
+        return float(np.max(self.data))
+
+    def copy(self):
+        return copy.deepcopy(self)
+
+    def fill(self, value: float, mask: np.ndarray):
+        mask_frames = ()
+        if mask.ndim == 4:
+            if mask.shape[0] != self.frame_count:
+                raise Exception("Mask frame count is not same as ")
+            for f in range(self.frame_count):
+                mask_frame = mask[f, :, :, :]
+                mask_frame = scipy.minimum_filter(
+                    mask_frame.astype(np.float32), size=3)
+                # mask_frame = scipy.median_filter(
+                #     mask_frame.astype(np.float32), size=2)
+                mask_frames += (mask_frame,)
+        elif mask.ndim == 3:
+            for f in range(self.frame_count):
+                mask_frame = mask[:, :, :]
+                mask_frame = scipy.minimum_filter(
+                    mask_frame.astype(np.float32), size=3)
+                # mask_frame = scipy.median_filter(
+                #     mask_frame.astype(np.float32), size=2)
+                mask_frames += (mask_frame,)
+        else:
+            raise Exception("Mask shape order should be TXYZ or XYZ")
+
+        _mask = np.stack(mask_frames)
+        _mask = np.expand_dims(_mask, axis=-1)
+        self.data = _mask * value + (1-_mask) * self.data
+
+    def resize(self, shape: tuple, progress_callback=None):
+        if len(shape) != 3:
+            raise Exception("Shape must be 3 dim")
+
+        data = self.data
+        order = 0 if self.dtype == bool else 1
+
+        # TXYZC > TXYZ
+        if self.kind in ['label', 'scalar']:
+            data = np.amax(data, -1)
+
+        # if self.kind in ['scalar']:
+        #     dtype = data.dtype
+            # data = data.astype(np.float32)
+
+        data_frames = ()
+        for f in range(self.frame_count):
+            if progress_callback:
+                progress_callback(f, self.frame_count)
+
+            # frame = ski.resize(data[f, :, :, :],
+            #                    shape,
+            #                    preserve_range=True,
+            #                    anti_aliasing=data.dtype.kind != "b")
+
+            factors = np.divide(self.shape, shape)
+            zoom_factors = [1 / f for f in factors]
+            frame = ndi.zoom(data[f, :, :, :],
+                             zoom_factors,
+                             order=order)
+
+            data_frames += (frame,)
+
+        data = np.stack(data_frames)
+
+        # if self.kind in ['scalar']:
+        #     data = data.astype(dtype)
+
+        # TXYZ > TXYZC
+        if self.kind in ['label', 'scalar']:
+            data = np.expand_dims(data, axis=-1)  # expend channel
+
+        self.data = data

bioxelnodes/bioxel/parse.py

@@ -0,0 +1,393 @@
+from pathlib import Path
+import numpy as np
+from .layer import Layer
+
+# 3rd-party
+import SimpleITK as sitk
+from pyometiff import OMETIFFReader
+import mrcfile
+import transforms3d
+
+
+"""
+Convert any volumetric data to 3D numpy array with order TXYZC
+"""
+
+SUPPORT_EXTS = ['', '.dcm', '.DCM', '.DICOM', '.ima', '.IMA',
+                '.ome.tiff', '.ome.tif',
+                '.tif', '.TIF', '.tiff', '.TIFF',
+                '.mrc', '.mrc.gz', '.map', '.map.gz',
+                '.bmp', '.BMP',
+                '.png', '.PNG',
+                '.jpg', '.JPG', '.jpeg', '.JPEG',
+                '.PIC', '.pic',
+                '.gipl', '.gipl.gz',
+                '.lsm', '.LSM',
+                '.mnc', '.MNC',
+                '.mrc', '.rec',
+                '.mha', '.mhd',
+                '.hdf', '.h4', '.hdf4', '.he2', '.h5', '.hdf5', '.he5',
+                '.nia', '.nii', '.nii.gz', '.hdr', '.img', '.img.gz',
+                '.nrrd', '.nhdr',
+                '.vtk',
+                '.gz']
+
+OME_EXTS = ['.ome.tiff', '.ome.tif',
+            '.tif', '.TIF', '.tiff', '.TIFF']
+
+MRC_EXTS = ['.mrc', '.mrc.gz', '.map', '.map.gz']
+
+DICOM_EXTS = ['', '.dcm', '.DCM', '.DICOM', '.ima', '.IMA']
+
+SEQUENCE_EXTS = ['.bmp', '.BMP',
+                 '.jpg', '.JPG', '.jpeg', '.JPEG',
+                 '.tif', '.TIF', '.tiff', '.TIFF',
+                 '.png', '.PNG']
+
+
+def get_ext(filepath: Path) -> str:
+    if filepath.name.endswith(".nii.gz"):
+        return ".nii.gz"
+    elif filepath.name.endswith(".img.gz"):
+        return ".img.gz"
+    elif filepath.name.endswith(".gipl.gz"):
+        return ".gipl.gz"
+    elif filepath.name.endswith(".ome.tiff"):
+        return ".ome.tiff"
+    elif filepath.name.endswith(".ome.tif"):
+        return ".ome.tif"
+    elif filepath.name.endswith(".mrc.gz"):
+        return ".mrc.gz"
+    elif filepath.name.endswith(".map.gz"):
+        return ".map.gz"
+    else:
+        return filepath.suffix
+
+
+def get_file_name(filepath: Path):
+    ext = get_ext(filepath)
+    return filepath.name.removesuffix(ext).replace(" ", "-")
+
+
+def get_file_number(filepath: Path) -> str:
+    name = get_file_name(filepath)
+    digits = ""
+
+    # Iterate through the characters in reverse order
+    started = False
+    for char in name[::-1]:
+        if char.isdigit():
+            started = True
+            # If the character is a digit, add it to the digits string
+            digits += char
+        else:
+            if started:
+                # If a non-digit character is encountered, stop the loop
+                break
+
+    # Reverse the digits string to get the correct order
+    return digits[::-1]
+
+
+def get_sequence_name(filepath: Path) -> str:
+    name = get_file_name(filepath)
+    number = get_file_number(filepath)
+    return name.removesuffix(number)
+
+
+def get_sequence_index(filepath: Path) -> int:
+    number = get_file_number(filepath)
+    return int(number) if number != "" else 0
+
+
+def collect_sequence(filepath: Path):
+    file_dict = {}
+    for f in filepath.parent.iterdir():
+        if f.is_file() \
+                and get_ext(filepath) == get_ext(f) \
+                and get_sequence_name(filepath) == get_sequence_name(f):
+            index = get_sequence_index(f)
+            file_dict[index] = f
+
+    # reomve isolated seq file
+    for key in file_dict.copy().keys():
+        if not file_dict.get(key+1) \
+                and not file_dict.get(key-1):
+            del file_dict[key]
+
+    file_dict = dict(sorted(file_dict.items()))
+    sequence = [str(f) for f in file_dict.values()]
+
+    if len(sequence) == 0:
+        sequence = [str(filepath)]
+
+    return sequence
+
+
+def parse_volumetric_data(data_file: str, series_id="", progress_callback=None) -> Layer:
+    """Parse any volumetric data to numpy with shap (T,X,Y,Z,C)
+
+    Args:
+        data_file (str): file path
+        series_id (str, optional): DICOM series id. Defaults to "".
+
+    Returns:
+        _type_: _description_
+    """
+
+    data_path = Path(data_file).resolve()
+    ext = get_ext(data_path)
+
+    if progress_callback:
+        progress_callback(0, "Reading the Data...")
+
+    is_sequence = False
+    if ext in SEQUENCE_EXTS:
+        sequence = collect_sequence(data_path)
+        if len(sequence) > 1:
+            is_sequence = True
+
+    data = None
+    name = "",
+    description = ""
+    affine = np.identity(4)
+    spacing = (1, 1, 1)
+    origin = (0, 0, 0)
+    direction = (1, 0, 0, 0, 1, 0, 0, 0, 1)
+
+    # Parsing with mrcfile
+    if data is None and ext in MRC_EXTS and not is_sequence:
+        print("Parsing with mrcfile...")
+        # TODO: much to do with mrc
+        with mrcfile.open(data_path, 'r') as mrc:
+            data = mrc.data
+            # mrc.print_header()
+            # print(data.shape)
+            # print(mrc.voxel_size)
+
+            if mrc.is_single_image():
+                data = np.expand_dims(data, axis=0)  # expend frame
+                data = np.expand_dims(data, axis=-1)  # expend Z
+                data = np.expand_dims(data, axis=-1)  # expend channel
+
+            elif mrc.is_image_stack():
+                data = np.expand_dims(data, axis=-1)  # expend Z
+                data = np.expand_dims(data, axis=-1)  # expend channel
+
+            elif mrc.is_volume():
+                data = np.expand_dims(data, axis=0)  # expend frame
+                data = np.expand_dims(data, axis=-1)  # expend channel
+
+            elif mrc.is_volume_stack():
+                data = np.expand_dims(data, axis=-1)  # expend channel
+
+            name = get_file_name(data_path)
+            spacing = (mrc.voxel_size.x,
+                       mrc.voxel_size.y,
+                       mrc.voxel_size.z)
+
+    # Parsing with OMETIFFReader
+    if data is None and ext in OME_EXTS and not is_sequence:
+        print("Parsing with OMETIFFReader...")
+        reader = OMETIFFReader(fpath=data_path)
+        ome_image, metadata, xml_metadata = reader.read()
+
+        # TODO: some old bio-format tiff the header is not the same.
+        if progress_callback:
+            progress_callback(0.5, "Transpose to 'TXYZC'...")
+
+        try:
+            # print(ome_image.shape)
+            # for key in metadata:
+            #     print(f"{key},{metadata[key]}")
+            ome_order = metadata['DimOrder BF Array']
+            if ome_image.ndim == 2:
+                ome_order = ome_order.replace("T", "")\
+                    .replace("C", "").replace("Z", "")
+                bioxel_order = (ome_order.index('X'),
+                                ome_order.index('Y'))
+                data = np.transpose(ome_image, bioxel_order)
+                data = np.expand_dims(data, axis=0)  # expend frame
+                data = np.expand_dims(data, axis=-1)  # expend Z
+                data = np.expand_dims(data, axis=-1)  # expend channel
+
+            elif ome_image.ndim == 3:
+                # -> XYZC
+                ome_order = ome_order.replace("T", "").replace("C", "")
+                bioxel_order = (ome_order.index('X'),
+                                ome_order.index('Y'),
+                                ome_order.index('Z'))
+                data = np.transpose(ome_image, bioxel_order)
+                data = np.expand_dims(data, axis=0)  # expend frame
+                data = np.expand_dims(data, axis=-1)  # expend channel
+            elif ome_image.ndim == 4:
+                # -> XYZC
+                ome_order = ome_order.replace("T", "")
+                bioxel_order = (ome_order.index('X'),
+                                ome_order.index('Y'),
+                                ome_order.index('Z'),
+                                ome_order.index('C'))
+                data = np.transpose(ome_image, bioxel_order)
+                data = np.expand_dims(data, axis=0)  # expend frame
+            elif ome_image.ndim == 5:
+                # -> TXYZC
+                bioxel_order = (ome_order.index('T'),
+                                ome_order.index('X'),
+                                ome_order.index('Y'),
+                                ome_order.index('Z'),
+                                ome_order.index('C'))
+                data = np.transpose(ome_image, bioxel_order)
+
+            try:
+                spacing = (metadata['PhysicalSizeX'],
+                           metadata['PhysicalSizeY'],
+                           metadata['PhysicalSizeZ'])
+            except:
+                ...
+
+            name = get_file_name(data_path)
+        except:
+            ...
+
+    # Parsing with SimpleITK
+    if data is None:
+        print("Parsing with SimpleITK...")
+        if ext in DICOM_EXTS:
+            data_dirpath = data_path.parent
+            reader = sitk.ImageSeriesReader()
+            reader.MetaDataDictionaryArrayUpdateOn()
+            reader.LoadPrivateTagsOn()
+            series_files = reader.GetGDCMSeriesFileNames(
+                str(data_dirpath), series_id)
+            reader.SetFileNames(series_files)
+
+            itk_image = reader.Execute()
+            # for k in reader.GetMetaDataKeys(0):
+            #     v = reader.GetMetaData(0, k)
+            #     print(f'({k}) = = "{v}"')
+
+            def get_meta(key):
+                try:
+                    stirng = reader.GetMetaData(0, key).removesuffix(" ")
+                    if stirng in ["No study description",
+                                  "No series description",
+                                  ""]:
+                        return None
+                    else:
+                        return stirng
+                except:
+                    return None
+
+            study_description = get_meta("0008|1030")
+            series_description = get_meta("0008|103e")
+            series_modality = get_meta("0008|0060")
+
+            name = study_description or data_dirpath.name
+            if series_description and series_modality:
+                description = f"{series_description}-{series_modality}"
+            elif series_description:
+                description = series_description
+            elif series_modality:
+                description = series_modality
+            else:
+                description = ""
+
+            name = name.replace(" ", "-")
+            description = description.replace(" ", "-")
+
+        elif ext in SEQUENCE_EXTS and is_sequence:
+            itk_image = sitk.ReadImage(sequence)
+            name = get_sequence_name(data_path)
+        else:
+            itk_image = sitk.ReadImage(data_path)
+            name = get_file_name(data_path)
+
+        # for key in itk_image.GetMetaDataKeys():
+        #     print(f"{key},{itk_image.GetMetaData(key)}")
+
+        if progress_callback:
+            progress_callback(0.5, "Transpose to 'TXYZC'...")
+
+        if itk_image.GetDimension() == 2:
+
+            data = sitk.GetArrayFromImage(itk_image)
+
+            if data.ndim == 3:
+                data = np.transpose(data, (1, 0, 2))
+
+                data = np.expand_dims(data, axis=-2)  # expend Z
+            else:
+                data = np.transpose(data)
+                data = np.expand_dims(data, axis=-1)  # expend Z
+                data = np.expand_dims(data, axis=-1)  # expend channel
+
+            data = np.expand_dims(data, axis=0)  # expend frame
+
+        elif itk_image.GetDimension() == 3:
+            if ext not in SEQUENCE_EXTS:
+                itk_image = sitk.DICOMOrient(itk_image, 'RAS')
+                # After sitk.DICOMOrient(), origin and direction will also orient base on LPS
+                # so we need to convert them into RAS
+                # affine = axis_conversion(from_forward='-Z',
+                #                          from_up='-Y',
+                #                          to_forward='-Z',
+                #                          to_up='Y').to_4x4()
+
+                affine = np.array([[-1.0000,  0.0000, 0.0000, 0.0000],
+                                   [0.0000, -1.0000, 0.0000, 0.0000],
+                                   [0.0000,  0.0000, 1.0000, 0.0000],
+                                   [0.0000,  0.0000, 0.0000, 1.0000]])
+
+            spacing = tuple(itk_image.GetSpacing())
+            origin = tuple(itk_image.GetOrigin())
+            direction = tuple(itk_image.GetDirection())
+
+            data = sitk.GetArrayFromImage(itk_image)
+            # transpose ijk to kji
+            if data.ndim == 4:
+                data = np.transpose(data, (2, 1, 0, 3))
+            else:
+                data = np.transpose(data)
+                data = np.expand_dims(data, axis=-1)  # expend channel
+
+            data = np.expand_dims(data, axis=0)  # expend frame
+
+        elif itk_image.GetDimension() == 4:
+
+            spacing = tuple(itk_image.GetSpacing()[:3])
+            origin = tuple(itk_image.GetOrigin()[:3])
+            # FIXME: not sure...
+            direction = np.array(itk_image.GetDirection())
+            direction = direction.reshape(3, 3) if itk_image.GetDimension() == 3 \
+                else direction.reshape(4, 4)
+
+            direction = direction[1:, 1:]
+            direction = tuple(direction.flatten())
+
+            data = sitk.GetArrayFromImage(itk_image)
+
+            if data.ndim == 5:
+                data = np.transpose(data, (0, 3, 2, 1, 4))
+            else:
+                data = np.transpose(data, (0, 3, 2, 1))
+                data = np.expand_dims(data, axis=-1)
+
+        if itk_image.GetDimension() > 5:
+            raise Exception
+
+    t = origin
+    r = np.array(direction).reshape((3, 3))
+    affine = np.dot(affine,
+                    transforms3d.affines.compose(t, r, [1, 1, 1]))
+
+    meta = {
+        "name": name,
+        "description": description,
+        "spacing": spacing,
+        "affine": affine,
+        "xyz_shape": data.shape[1:4],
+        "frame_count": data.shape[0],
+        "channel_count": data.shape[-1],
+    }
+
+    return data, meta

bioxelnodes/bioxel/scipy/__init__.py

@@ -0,0 +1,5 @@
+from ._interpolation import zoom
+from ._filters import (gaussian_filter,
+                       median_filter,
+                       maximum_filter,
+                       minimum_filter)

bioxelnodes/bioxelutils/container.py

@@ -0,0 +1,180 @@
+import bpy
+
+from ..bioxel.container import Container
+from bpy_extras.io_utils import axis_conversion
+from mathutils import Matrix, Vector
+
+
+from .layer import Layer, get_container_layer_objs, layer_to_obj, obj_to_layer
+from ..nodes import custom_nodes
+from .node import get_nodes_by_type, move_node_to_node
+
+
+NODE_TYPE = {
+    "label": "BioxelNodes_MaskByLabel",
+    "scalar": "BioxelNodes_MaskByThreshold"
+}
+
+
+def calc_bbox_verts(origin: tuple, size: tuple):
+    bbox_origin = Vector(
+        (origin[0], origin[1], origin[2]))
+    bbox_size = Vector(
+        (size[0], size[1], size[2]))
+    bbox_verts = [
+        (
+            bbox_origin[0] + 0,
+            bbox_origin[1] + 0,
+            bbox_origin[2] + 0
+        ),
+        (
+            bbox_origin[0] + 0,
+            bbox_origin[1] + 0,
+            bbox_origin[2] + bbox_size[2]
+        ),
+        (
+            bbox_origin[0] + 0,
+            bbox_origin[1] + bbox_size[1],
+            bbox_origin[2] + 0
+        ),
+        (
+            bbox_origin[0] + 0,
+            bbox_origin[1] + bbox_size[1],
+            bbox_origin[2] + bbox_size[2]
+        ),
+        (
+            bbox_origin[0] + bbox_size[0],
+            bbox_origin[1] + 0,
+            bbox_origin[2] + 0
+        ),
+        (
+            bbox_origin[0] + bbox_size[0],
+            bbox_origin[1] + 0,
+            bbox_origin[2] + bbox_size[2],
+        ),
+        (
+            bbox_origin[0] + bbox_size[0],
+            bbox_origin[1] + bbox_size[1],
+            bbox_origin[2] + 0,
+        ),
+        (
+            bbox_origin[0] + bbox_size[0],
+            bbox_origin[1] + bbox_size[1],
+            bbox_origin[2] + bbox_size[2],
+        ),
+    ]
+    return bbox_verts
+
+
+def get_container_objs_from_selection():
+    container_objs = []
+    for obj in bpy.context.selected_objects:
+        if get_container_obj(obj):
+            container_objs.append(obj)
+
+    return list(set(container_objs))
+
+
+def get_container_obj(current_obj):
+    if current_obj:
+        if current_obj.get('bioxel_container'):
+            return current_obj
+        elif current_obj.get('bioxel_layer'):
+            parent = current_obj.parent
+            return parent if parent.get('bioxel_container') else None
+    return None
+
+
+def add_layers(layers: list[Layer],
+               container_obj: bpy.types.Object,
+               cache_dir: str):
+
+    container_node_group = container_obj.modifiers[0].node_group
+
+    for i, layer in enumerate(layers):
+        layer_obj = layer_to_obj(layer, container_obj, cache_dir)
+        mask_node = custom_nodes.add_node(container_node_group,
+                                          NODE_TYPE[layer.kind])
+        mask_node.label = layer_obj.name
+        mask_node.inputs[0].default_value = layer_obj
+
+        # Connect to output if no output linked
+        output_node = get_nodes_by_type(container_node_group,
+                                        'NodeGroupOutput')[0]
+        if len(output_node.inputs[0].links) == 0:
+            container_node_group.links.new(mask_node.outputs[0],
+                                           output_node.inputs[0])
+            move_node_to_node(mask_node, output_node, (-300, 0))
+        else:
+            move_node_to_node(mask_node, output_node, (0, -100 * (i+1)))
+
+    return container_obj
+
+
+def obj_to_container(container_obj: bpy.types.Object):
+    layer_objs = get_container_layer_objs(container_obj)
+    layers = [obj_to_layer(obj) for obj in layer_objs]
+    container = Container(name=container_obj.name,
+                          layers=layers)
+    return container
+
+
+def container_to_obj(container: Container,
+                     scene_scale: float,
+                     cache_dir: str):
+    # Wrapper a Container
+
+    # Make transformation
+    # (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 = Matrix.Scale(scene_scale,
+                                   4)
+
+    bpy.ops.mesh.primitive_cube_add(enter_editmode=False,
+                                    align='WORLD',
+                                    location=(0, 0, 0),
+                                    scale=(1, 1, 1))
+
+    container_obj = bpy.context.active_object
+
+    bbox_verts = calc_bbox_verts((0, 0, 0), container.layers[0].shape)
+    for i, vert in enumerate(container_obj.data.vertices):
+        transform = Matrix(container.layers[0].affine)
+        vert.co = transform @ Vector(bbox_verts[i])
+
+    container_obj.matrix_world = mat_ras2blender @ mat_scene_scale
+    container_obj.name = container.name
+    container_obj.data.name = container.name
+    container_obj.show_in_front = True
+    container_obj['bioxel_container'] = True
+
+    bpy.ops.node.new_geometry_nodes_modifier()
+    container_node_group = container_obj.modifiers[0].node_group
+    input_node = get_nodes_by_type(container_node_group,
+                                   'NodeGroupInput')[0]
+    container_node_group.links.remove(
+        input_node.outputs[0].links[0])
+
+    for i, layer in enumerate(container.layers):
+        layer_obj = layer_to_obj(layer, container_obj, cache_dir)
+        mask_node = custom_nodes.add_node(container_node_group,
+                                          NODE_TYPE[layer.kind])
+        mask_node.label = layer_obj.name
+        mask_node.inputs[0].default_value = layer_obj
+
+        # Connect to output if no output linked
+        output_node = get_nodes_by_type(container_node_group,
+                                        'NodeGroupOutput')[0]
+        if len(output_node.inputs[0].links) == 0:
+            container_node_group.links.new(mask_node.outputs[0],
+                                           output_node.inputs[0])
+            move_node_to_node(mask_node, output_node, (-300, 0))
+        else:
+            move_node_to_node(mask_node, output_node, (0, -100 * (i+1)))
+
+    return container_obj

bioxelnodes/bioxelutils/layer.py

@@ -0,0 +1,232 @@
+import random
+import re
+import bpy
+import numpy as np
+
+import pyopenvdb as vdb
+from pathlib import Path
+from uuid import uuid4
+
+from ..nodes import custom_nodes
+from ..bioxel.layer import Layer
+from .node import get_nodes_by_type, move_node_between_nodes
+
+
+def get_layer_obj(current_obj: bpy.types.Object):
+    if current_obj:
+        if current_obj.get('bioxel_layer') and current_obj.parent:
+            if current_obj.parent.get('bioxel_container'):
+                return current_obj
+    return None
+
+
+def get_container_layer_objs(container_obj: bpy.types.Object):
+    layer_objs = []
+    for obj in bpy.context.scene.objects:
+        if obj.parent == container_obj and get_layer_obj(obj):
+            layer_objs.append(obj)
+
+    return layer_objs
+
+
+def get_all_layer_objs():
+    layer_objs = []
+    for obj in bpy.context.scene.objects:
+        if get_layer_obj(obj):
+            layer_objs.append(obj)
+
+    return layer_objs
+
+
+def obj_to_layer(layer_obj: bpy.types.Object):
+    cache_filepath = Path(bpy.path.abspath(layer_obj.data.filepath)).resolve()
+    is_sequence = re.search(r'\.\d{4}\.',
+                            cache_filepath.name) is not None
+    if is_sequence:
+        cache_path = cache_filepath.parent
+        data_frames = ()
+        for f in cache_path.iterdir():
+            if not f.is_file() or f.suffix != ".vdb":
+                continue
+            grids, base_metadata = vdb.readAll(str(f))
+            grid = grids[0]
+            metadata = grid.metadata
+            data_frame = np.ndarray(grid["data_shape"], np.float32)
+            grid.copyToArray(data_frame)
+            data_frames += (data_frame,)
+        data = np.stack(data_frames)
+    else:
+        grids, base_metadata = vdb.readAll(str(cache_filepath))
+        grid = grids[0]
+        metadata = grid.metadata
+        data = np.ndarray(grid["data_shape"], np.float32)
+        grid.copyToArray(data)
+        data = np.expand_dims(data, axis=0)  # expend frame
+
+    name = metadata["layer_name"]
+    kind = metadata["layer_kind"]
+    affine = metadata["layer_affine"]
+    dtype = metadata.get("data_dtype") or "float32"
+    offset = metadata.get("data_offset") or 0
+    data = data - np.full_like(data, offset)
+    data = data.astype(dtype)
+
+    if kind in ["scalar", "label"]:
+        data = np.expand_dims(data, axis=-1)  # expend channel
+
+    layer = Layer(data=data,
+                  name=name,
+                  kind=kind,
+                  affine=affine)
+
+    return layer
+
+
+def layer_to_obj(layer: Layer,
+                 container_obj: bpy.types.Object,
+                 cache_dir: str):
+
+    data = layer.data
+
+    # TXYZC > TXYZ
+    if layer.kind in ['label', 'scalar']:
+        data = np.amax(data, -1)
+
+    offset = 0
+    if layer.kind in ['scalar']:
+        data = data.astype(np.float32)
+        orig_min = float(np.min(data))
+        if orig_min < 0:
+            offset = -orig_min
+
+        data = data + np.full_like(data, offset)
+
+    metadata = {
+        "layer_name": layer.name,
+        "layer_kind": layer.kind,
+        "layer_affine": layer.affine.tolist(),
+        "data_shape": layer.shape,
+        "data_dtype": layer.data.dtype.str,
+        "data_offset": offset
+    }
+
+    if layer.frame_count > 1:
+        print(f"Saving the Cache of {layer.name}...")
+        vdb_name = str(uuid4())
+        sequence_path = Path(cache_dir, vdb_name)
+        sequence_path.mkdir(parents=True, exist_ok=True)
+
+        cache_filepaths = []
+        for f in range(layer.frame_count):
+            grid = vdb.FloatGrid()
+            grid.copyFromArray(data[f, :, :, :].copy().astype(np.float32))
+            grid.transform = vdb.createLinearTransform(
+                layer.affine.transpose())
+            grid.metadata = metadata
+            grid.name = layer.kind
+
+            cache_filepath = Path(sequence_path,
+                                  f"{vdb_name}.{str(f+1).zfill(4)}.vdb")
+            vdb.write(str(cache_filepath), grids=[grid])
+            cache_filepaths.append(cache_filepath)
+
+        print(f"Loading the Cache of {layer.name}...")
+        files = [{"name": str(cache_filepath.name), "name": str(cache_filepath.name)}
+                 for cache_filepath in cache_filepaths]
+
+        bpy.ops.object.volume_import(filepath=str(cache_filepaths[0]),
+                                     directory=str(cache_filepaths[0].parent),
+                                     files=files, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
+
+    else:
+        grid = vdb.FloatGrid()
+        grid.copyFromArray(data[0, :, :, :].copy().astype(np.float32))
+        grid.transform = vdb.createLinearTransform(
+            layer.affine.transpose())
+        grid.metadata = metadata
+        grid.name = layer.kind
+
+        print(f"Saving the Cache of {layer.name}...")
+        cache_filepath = Path(cache_dir, f"{uuid4()}.vdb")
+        vdb.write(str(cache_filepath), grids=[grid])
+        cache_filepaths = [cache_filepath]
+
+        print(f"Loading the Cache of {layer.name}...")
+        bpy.ops.object.volume_import(filepath=str(cache_filepaths[0]),
+                                     align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
+
+    layer_obj = bpy.context.active_object
+    layer_obj.data.sequence_mode = 'REPEAT'
+
+    # Set props to VDB object
+    layer_obj.name = f"{container_obj.name}_{layer.name}"
+    layer_obj.data.name = f"{container_obj.name}_{layer.name}"
+
+    layer_obj.lock_location[0] = True
+    layer_obj.lock_location[1] = True
+    layer_obj.lock_location[2] = True
+    layer_obj.lock_rotation[0] = True
+    layer_obj.lock_rotation[1] = True
+    layer_obj.lock_rotation[2] = True
+    layer_obj.lock_scale[0] = True
+    layer_obj.lock_scale[1] = True
+    layer_obj.lock_scale[2] = True
+
+    layer_obj.visible_camera = False
+    layer_obj.visible_diffuse = False
+    layer_obj.visible_glossy = False
+    layer_obj.visible_transmission = False
+    layer_obj.visible_volume_scatter = False
+    layer_obj.visible_shadow = False
+
+    layer_obj.hide_select = True
+    layer_obj.hide_render = True
+    layer_obj.hide_viewport = True
+
+    layer_obj['bioxel_layer'] = True
+    layer_obj.parent = container_obj
+
+    for collection in layer_obj.users_collection:
+        collection.objects.unlink(layer_obj)
+
+    for collection in container_obj.users_collection:
+        collection.objects.link(layer_obj)
+
+    print(f"Creating Node for {layer.name}...")
+    bpy.ops.node.new_geometry_nodes_modifier()
+    node_group = layer_obj.modifiers[0].node_group
+    layer_node = custom_nodes.add_node(node_group,
+                                          "BioxelNodes__Layer")
+
+    layer_node.inputs['name'].default_value = layer.name
+    layer_node.inputs['shape'].default_value = layer.shape
+    layer_node.inputs['kind'].default_value = layer.kind
+
+    for i in range(layer.affine.shape[1]):
+        for j in range(layer.affine.shape[0]):
+            affine_key = f"affine{i}{j}"
+            layer_node.inputs[affine_key].default_value = layer.affine[j, i]
+
+    layer_node.inputs['id'].default_value = random.randint(-200000000,
+                                                              200000000)
+    layer_node.inputs['bioxel_size'].default_value = layer.bioxel_size[0]
+    layer_node.inputs['dtype'].default_value = layer.dtype.str
+    layer_node.inputs['dtype_num'].default_value = layer.dtype.num
+    layer_node.inputs['offset'].default_value = max(0, -layer.min)
+    layer_node.inputs['min'].default_value = layer.min
+    layer_node.inputs['max'].default_value = layer.max
+
+    input_node = get_nodes_by_type(node_group,
+                                   'NodeGroupInput')[0]
+    output_node = get_nodes_by_type(node_group,
+                                    'NodeGroupOutput')[0]
+
+    node_group.links.new(input_node.outputs[0],
+                         layer_node.inputs[0])
+    node_group.links.new(layer_node.outputs[0],
+                         output_node.inputs[0])
+
+    move_node_between_nodes(
+        layer_node, [input_node, output_node])
+
+    return layer_obj

bioxelnodes/bioxelutils/node.py

@@ -0,0 +1,26 @@
+def move_node_to_node(node, target_node, offset=(0, 0)):
+    node.location.x = target_node.location.x + offset[0]
+    node.location.y = target_node.location.y + offset[1]
+
+
+def move_node_between_nodes(node, target_nodes, offset=(0, 0)):
+    xs = []
+    ys = []
+    for target_node in target_nodes:
+        xs.append(target_node.location.x)
+        ys.append(target_node.location.y)
+
+    node.location.x = sum(xs) / len(xs) + offset[0]
+    node.location.y = sum(ys) / len(ys) + offset[1]
+
+
+def get_node_type(node):
+    node_type = type(node).__name__
+    if node_type == "GeometryNodeGroup":
+        node_type = node.node_tree.name
+
+    return node_type
+
+
+def get_nodes_by_type(node_group, type_name: str):
+    return [node for node in node_group.nodes if get_node_type(node) == type_name]

bioxelnodes/blender_manifest.toml

@@ -0,0 +1,38 @@
+schema_version = "1.0.0"
+
+id = "bioxelnodes"
+version = "0.3.3"
+name = "Bioxel Nodes"
+tagline = "For scientific volumetric data visualization in Blender"
+maintainer = "Ma Nan <icrdr2010@outlook.com>"
+type = "add-on"
+website = "https://omoolab.github.io/BioxelNodes/latest"
+
+tags = ["Geometry Nodes", "Render", "Import-Export"]
+blender_version_min = "4.2.0"
+license = ["SPDX:MIT"]
+copyright = ["2024 OmooLab"]
+platforms = ["windows-x64", "linux-x64", "macos-arm64", "macos-x64"]
+
+wheels = [
+  "./wheels/SimpleITK-2.3.1-cp311-cp311-win_amd64.whl",
+  "./wheels/SimpleITK-2.3.1-cp311-cp311-macosx_10_9_x86_64.whl",
+  "./wheels/SimpleITK-2.3.1-cp311-cp311-macosx_11_0_arm64.whl",
+  "./wheels/SimpleITK-2.3.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
+  "./wheels/lxml-5.2.2-cp311-cp311-win_amd64.whl",
+  "./wheels/lxml-5.2.2-cp311-cp311-macosx_10_9_arm64.whl",
+  "./wheels/lxml-5.2.2-cp311-cp311-macosx_10_9_x86_64.whl",
+  "./wheels/lxml-5.2.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
+  "./wheels/h5py-3.11.0-cp311-cp311-win_amd64.whl",
+  "./wheels/h5py-3.11.0-cp311-cp311-macosx_11_0_arm64.whl",
+  "./wheels/h5py-3.11.0-cp311-cp311-macosx_10_9_x86_64.whl",
+  "./wheels/h5py-3.11.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
+  "./wheels/tifffile-2024.7.24-py3-none-any.whl",
+  "./wheels/pyometiff-1.0.0-py3-none-any.whl",
+  "./wheels/mrcfile-1.5.1-py2.py3-none-any.whl",
+  "./wheels/transforms3d-0.4.2-py3-none-any.whl",
+]
+
+[permissions]
+files = "Import/export volume data from/to disk"
+

bioxelnodes/customnodes/menus.py

@@ -1,4 +1,3 @@
-import shutil
 import bpy
 from pathlib import Path
 from .nodes import AddCustomNode

bioxelnodes/customnodes/nodes.py

@@ -94,6 +94,7 @@ class AddCustomNode():
         self.get_node_tree(self.node_type, self.node_link)
         node = node_group.nodes.new("GeometryNodeGroup")
         self.assign_node_tree(node)
+        node.show_options = False
 
         return node
 
@@ -121,5 +122,6 @@ class CUSTOMNODES_OT_Add_Custom_Node(bpy.types.Operator, AddCustomNode):
         node = bpy.context.active_node
 
         self.assign_node_tree(node)
+        node.show_options = False
 
         return {"FINISHED"}

bioxelnodes/exceptions.py

@@ -0,0 +1,4 @@
+class CancelledByUser(Exception):
+    def __init__(self):
+        message = 'Cancelled by user'
+        super().__init__(message)

bioxelnodes/externalpackage/__init__.py

@@ -1,2 +0,0 @@
-from .preferences import ExternalPackagePreferences
-from .package import PackageInstaller

bioxelnodes/externalpackage/package.py

@@ -1,393 +0,0 @@
-"""
-Handling installation of external python packages inside of Blender's bundled python.
-"""
-import subprocess
-import sys
-import logging
-from importlib.metadata import version as get_version, PackageNotFoundError
-import bpy
-from pathlib import Path
-
-ADDON_NAME = __package__.split(".")[0]
-
-PYPI_MIRROR = {
-    # the original.
-    'Default': '',
-    # two mirrors in China Mainland to help those poor victims under GFW.
-    'BFSU (Beijing)': 'https://mirrors.bfsu.edu.cn/pypi/web/simple',
-    'TUNA (Beijing)': 'https://pypi.tuna.tsinghua.edu.cn/simple',
-    # append more if necessary.
-}
-
-
-class InstallationError(Exception):
-    """
-    Exception raised when there is an error installing a package.
-
-    Attributes
-    ----------
-    package_name : str
-        The name of the package that failed to install.
-    error_message : str
-        The error message returned by pip.
-
-    """
-
-    def __init__(self, package_name, error_message):
-        self.package_name = package_name
-        self.error_message = error_message
-        super().__init__(f"Failed to install {package_name}: {error_message}")
-
-
-class PackageInstaller():
-    def __init__(
-        self,
-        requirements_dir: str,
-        log_dir: str = None,
-        pypi_mirror_provider='Default',
-    ) -> None:
-        self.pypi_mirror_provider = pypi_mirror_provider
-        self.log_path: Path = Path(log_dir) if log_dir \
-            else Path.home() / '.externalpackage' / 'logs'
-        self.requirements_path: Path = Path(requirements_dir)
-
-    def start_logging(self, logfile_name: str = 'side-packages-install') -> logging.Logger:
-        """
-        Configure and start logging to a file.
-
-        Parameters
-        ----------
-        logfile_name : str, optional
-            The name of the log file. Defaults to 'side-packages-install'.
-
-        Returns
-        -------
-        logging.Logger
-            A Logger object that can be used to write log messages.
-
-        This function sets up a logging configuration with a specified log file name and logging level.
-        The log file will be created in the `ADDON_DIR/logs` directory. If the directory
-        does not exist, it will be created. The function returns a Logger object that can be used to
-        write log messages.
-
-        """
-        # Create the logs directory if it doesn't exist
-        self.log_path.mkdir(parents=True, exist_ok=True)
-
-        # Set up logging configuration
-        logfile_path = Path(self.log_path, f"{logfile_name}.log")
-        logging.basicConfig(filename=logfile_path,
-                            level=logging.INFO, encoding='utf-8')
-
-        # Return logger object
-        return logging.getLogger()
-
-    @property
-    def pypi_mirror_url(self) -> str:
-        """
-        Process a PyPI mirror provider and return the corresponding URL.
-
-        Parameters
-        ----------
-        pypi_mirror_provider : str
-            The PyPI mirror provider to process.
-
-        Returns
-        -------
-        str
-            The URL of the PyPI mirror.
-
-        Raises
-        ------
-        ValueError
-            If the provided PyPI mirror provider is invalid.
-
-        """
-        if self.pypi_mirror_provider.startswith('https:'):
-            return self.pypi_mirror_provider
-        elif self.pypi_mirror_provider in PYPI_MIRROR.keys():
-            return PYPI_MIRROR[self.pypi_mirror_provider]
-        else:
-            raise ValueError(
-                f"Invalid PyPI mirror provider: {self.pypi_mirror_provider}")
-
-    @property
-    def packages(self) -> dict:
-        """
-        Read a requirements file and extract package information into a dictionary.
-
-        Parameters
-        ----------
-        requirements : str, optional
-            The path to the requirements file. If not provided, the function looks for a `requirements.txt`
-            file in the same directory as the script.
-
-        Returns
-        -------
-        dict
-            A dictionary containing package information. Each element of the dictionary is a dictionary containing the package name, version, and description.
-
-        Example
-        -------
-        Given the following requirements file:
-        ```python
-        Flask==1.1.2 # A micro web framework for Python
-        pandas==1.2.3 # A fast, powerful, flexible, and easy-to-use data analysis and manipulation tool
-        numpy==1.20.1 # Fundamental package for scientific computing
-        ```
-        The function would return the following dictionary:
-        ```python
-        [
-            {
-                "package": "Flask",
-                "version": "1.1.2",
-                "description": "A micro web framework for Python"
-            },
-            {
-                "package": "pandas",
-                "version": "1.2.3",
-                "description": "A fast, powerful, flexible, and easy-to-use data analysis and manipulation tool"
-            },
-            {
-                "package": "numpy",
-                "version": "1.20.1",
-                "description": "Fundamental package for scientific computing"
-            }
-        ]
-        ```
-        """
-        requirements_filepath = self.requirements_path / "requirements.txt"
-        if requirements_filepath.is_file():
-            with requirements_filepath.open('r') as f:
-                lines = f.read().splitlines()
-                packages = {}
-                for line in lines:
-                    try:
-                        package, description = line.split('#')
-                        package_meta = package.split('==')
-                        name = package_meta[0].strip()
-                        packages[name] = {
-                            "name": name,
-                            "version": package_meta[1].strip(),
-                            "description": description.strip()
-                        }
-                    except ValueError:
-                        # Skip line if it doesn't have the expected format
-                        pass
-            return packages
-        else:
-            raise FileNotFoundError(requirements_filepath)
-
-    def is_installed(self, package_name: str) -> bool:
-        """
-        Check if the specified package is installed and the version matches that specified
-        in the `requirements.txt` file.
-
-        Parameters
-        ----------
-        package : str
-            The name of the package to check.
-
-        Returns
-        -------
-        bool
-            True if the package is the current version, False otherwise.
-
-        """
-        package = self.packages.get(package_name)
-        try:
-            available_version = get_version(package['name'])
-            return available_version == package['version']
-        except PackageNotFoundError:
-            return False
-
-    def run_python(self, cmd_list: list = None, timeout: int = 600):
-        """
-        Runs pip command using the specified command list and returns the command output.
-
-        Parameters
-        ----------
-        cmd_list : list, optional
-            List of pip commands to be executed. Defaults to None.
-        mirror_url : str, optional
-            URL of a package repository mirror to be used for the command. Defaults to ''.
-        timeout : int, optional
-            Time in seconds to wait for the command to complete. Defaults to 600.
-
-        Returns
-        -------
-        tuple
-            A tuple containing the command list, command return code, command standard output,
-            and command standard error.
-
-        Example
-        -------
-        Install numpy using pip and print the command output
-        ```python
-        cmd_list = ["-m", "pip", "install", "numpy"]
-        mirror_url = 'https://pypi.org/simple/'
-        cmd_output = run_python(cmd_list, timeout=300)
-        print(cmd_output)
-        ```
-
-        """
-
-        # path to python.exe
-        python_exe = str(Path(sys.executable).resolve())
-
-        # build the command list
-        cmd_list = [python_exe] + cmd_list
-
-        # add mirror to the command list if it's valid
-        if self.pypi_mirror_url and self.pypi_mirror_url.startswith('https'):
-            cmd_list += ['-i', self.pypi_mirror_url]
-
-        log = self.start_logging()
-        log.info(f"Running Pip: '{cmd_list}'")
-
-        # run the command and capture the output
-        result = subprocess.run(cmd_list, timeout=timeout,
-                                stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-
-        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
-
-    def install_package(self, package: str) -> list:
-        """
-        Install a Python package and its dependencies using pip.
-
-        Parameters
-        ----------
-        package : str
-            The name of the package to install.
-        pypi_mirror_provider : str, optional
-            The name/url of the PyPI mirror provider to use. Default is 'Default'.
-
-        Returns
-        -------
-        list
-            A list of tuples containing the command list, return code, stdout, and stderr
-            for each pip command run.
-
-        Raises
-        ------
-        ValueError
-            If the package name is not provided.
-
-        Example
-        -------
-        To install the package 'requests' from the PyPI mirror 'MyMirror', use:
-        ```
-        install_package('requests', 'MyMirror')
-        ```
-
-        """
-        if not package:
-            raise ValueError("Package name must be provided.")
-
-        print(f"Installing {package}...")
-        print(f"Using PyPI mirror: {self.pypi_mirror_provider}")
-
-        self.run_python(["-m", "ensurepip"]),
-        self.run_python(["-m", "pip", "install", "--upgrade", "pip"])
-        result = self.run_python(["-m", "pip", "install", package, "--user"])
-
-        return result
-
-    def install_all_packages(self, pypi_mirror_provider: str = 'Default') -> list:
-        """
-        Install all packages listed in the 'requirements.txt' file.
-
-        Parameters
-        ----------
-        pypi_mirror_provider : str, optional
-            The PyPI mirror to use for package installation. Defaults to 'Default',
-            which uses the official PyPI repository.
-
-        Returns
-        -------
-        list
-            A list of tuples containing the installation results for each package.
-
-        Raises
-        ------
-        InstallationError
-            If there is an error during package installation.
-
-        Example
-        -------
-        To install all packages listed in the 'requirements.txt' file, run the following command:
-        ```
-        install_all_packages(pypi_mirror_provider='https://pypi.org/simple/')
-        ```
-
-        """
-        results = []
-        for package in self.packages.items():
-
-            try:
-                result = self.install_package(
-                    package=f"{package.get('name')}=={package.get('version')}"
-                )
-                results.append(result)
-            except InstallationError as e:
-                raise InstallationError(
-                    f"Error installing package {package.get('name')}: {str(e)}")
-        return results
-
-
-class EXTERNALPACKAGE_OT_Install_Package(bpy.types.Operator):
-    bl_idname = 'externalpackage.install_package'
-    bl_label = 'Install Given Python Package'
-    bl_options = {'REGISTER', 'INTERNAL'}
-
-    package: bpy.props.StringProperty(
-        name='Python Package',
-        description='Python Package to Install'
-    )  # type: ignore
-
-    version: bpy.props.StringProperty(
-        name='Python Package',
-        description='Python Package to Install'
-    )  # type: ignore
-
-    description: bpy.props.StringProperty(
-        name='Operator description',
-        default='Install specified python package.'
-    )  # type: ignore
-
-    @classmethod
-    def description(cls, context, properties):
-        return properties.description
-
-    def execute(self, context):
-        preferences = context.preferences.addons[ADDON_NAME].preferences
-        installer = PackageInstaller(
-            pypi_mirror_provider=preferences.pypi_mirror_provider,
-            log_dir=preferences.log_dir,
-            requirements_dir=preferences.requirements_dir
-        )
-
-        result = installer.install_package(f"{self.package}=={self.version}")
-        if result.returncode == 0 or installer.is_installed(self.package):
-            self.report(
-                {'INFO'},
-                f"Successfully installed {self.package} v{self.version}"
-            )
-        else:
-            self.report(
-                {'ERROR'},
-                f"""Error installing package. Please check the log files
-in {preferences.log_dir}."""
-            )
-        return {'FINISHED'}

bioxelnodes/externalpackage/preferences.py

@@ -1,95 +0,0 @@
-import bpy
-import subprocess
-from pathlib import Path
-from .package import PackageInstaller, PYPI_MIRROR
-
-# Defines the preferences panel for the addon, which shows the buttons for
-# installing and reinstalling the required python packages defined in 'requirements.txt'
-
-
-def get_pypi_mirrors(self, context, edit_text):
-    return PYPI_MIRROR.keys()
-
-
-class RebootBlender(bpy.types.Operator):
-    bl_idname = "externalpackage.reboot_blender"
-    bl_label = "Reboot Blender"
-    bl_description = "Reboot Blender"
-    bl_options = {'UNDO'}
-
-    def invoke(self, context, event):
-        context.window_manager.invoke_confirm(self, event)
-        return {'RUNNING_MODAL'}
-    
-    def execute(self, context):
-        blender_launcher = Path(
-            bpy.app.binary_path).parent / "blender-launcher.exe"
-        subprocess.run([str(blender_launcher), "-con", "--python-expr",
-                       "import bpy; bpy.ops.wm.recover_last_session()"])
-        bpy.ops.wm.quit_blender()
-        return {'FINISHED'}
-
-
-class ExternalPackagePreferences():
-    requirements_dir: bpy.props.StringProperty(
-        name="requirements.txt Directory",
-        subtype='DIR_PATH',
-        default=str(Path(__file__).parent)
-    )  # type: ignore
-
-    log_dir: bpy.props.StringProperty(
-        name="Python Log Directory",
-        subtype='DIR_PATH',
-        default=str(Path(Path.home(), '.externalpackage', 'logs'))
-    )  # type: ignore
-
-    pypi_mirror_provider: bpy.props.StringProperty(
-        name='pypi_mirror_provider',
-        description='PyPI Mirror Provider',
-        options={'TEXTEDIT_UPDATE', 'LIBRARY_EDITABLE'},
-        default='Default',
-        subtype='NONE',
-        search=get_pypi_mirrors,
-    )  # type: ignore
-
-    def draw(self, context):
-        layout = self.layout
-        layout.label(
-            text='**Install the required packages, then hit "Reboot Blender"**')
-
-        col_main = layout.column(heading='', align=False)
-        row_import = col_main.row()
-        row_import.prop(self, 'pypi_mirror_provider', text='PyPI Mirror')
-
-        installer = PackageInstaller(
-            pypi_mirror_provider=self.pypi_mirror_provider,
-            log_dir=self.log_dir,
-            requirements_dir=self.requirements_dir
-        )
-
-        for package in installer.packages.values():
-
-            name = package.get('name')
-            version = package.get('version')
-            description = package.get('description')
-
-            if installer.is_installed(name):
-                row = layout.row()
-                row.label(text=f"{name} version {version} is installed.")
-                op = row.operator('externalpackage.install_package',
-                                  text=f'Reinstall {name}')
-                op.package = name
-                op.version = version
-                op.description = f'Reinstall {name}'
-            else:
-                row = layout.row(heading=f"Package: {name}")
-                col = row.column()
-                col.label(text=str(description))
-                col = row.column()
-                op = col.operator('externalpackage.install_package',
-                                  text=f'Install {name}')
-                op.package = name
-                op.version = version
-                op.description = f'Install required python package: {name}'
-
-        layout.operator(RebootBlender.bl_idname)

bioxelnodes/io.py

@@ -1,874 +0,0 @@
-import math
-import bpy
-import shutil
-from bpy_extras.io_utils import axis_conversion
-import pyopenvdb as vdb
-import numpy as np
-from pathlib import Path
-from uuid import uuid4
-import mathutils
-import random
-
-from . import skimage as ski
-from .nodes import custom_nodes
-from .props import BIOXELNODES_Series
-from .utils import (calc_bbox_verts, get_all_layers, get_container_from_selection, get_layer, get_text_index_str,
-                    get_nodes_by_type, hide_in_ray, lock_transform, move_node_between_nodes, move_node_to_node, save_vdb, save_vdbs, select_object, show_message)
-
-try:
-    import SimpleITK as sitk
-except:
-    ...
-
-SUPPORT_EXTS = ['', '.dcm', '.DCM', '.DICOM',
-                '.bmp', '.BMP',
-                '.PIC', '.pic',
-                '.gipl', '.gipl.gz',
-                '.jpg', '.JPG', '.jpeg', '.JPEG',
-                '.lsm', '.LSM',
-                '.tif', '.TIF', '.tiff', '.TIFF',
-                '.mnc', '.MNC',
-                '.mrc', '.rec',
-                '.mha', '.mhd',
-                '.hdf', '.h4', '.hdf4', '.he2', '.h5', '.hdf5', '.he5',
-                '.nia', '.nii', '.nii.gz', '.hdr', '.img', '.img.gz',
-                '.nrrd', '.nhdr',
-                '.png', '.PNG',
-                '.vtk']
-
-SEQUENCE_EXTS = ['.dcm', '.DCM', '.DICOM',
-                 '.bmp', '.BMP',
-                 '.jpg', '.JPG', '.jpeg', '.JPEG',
-                 '.tif', '.TIF', '.tiff', '.TIFF',
-                 '.png', '.PNG']
-
-DICOM_EXTS = ['', '.dcm', '.DCM', '.DICOM']
-
-FH_EXTS = ['', '.dcm', '.DCM', '.DICOM',
-           '.gipl', '.gipl.gz',
-           '.mnc', '.MNC',
-           '.mrc', '.rec',
-           '.mha', '.mhd',
-           '.nia', '.nii', '.nii.gz', '.hdr', '.img', '.img.gz',
-           '.hdf', '.h4', '.hdf4', '.he2', '.h5', '.hdf5', '.he5',
-           '.nrrd', '.nhdr',
-           '.vtk',
-           '.gz']
-
-
-def get_layer_shape(bioxel_size: float, orig_shape: tuple, orig_spacing: tuple):
-    shape = (int(orig_shape[0] / bioxel_size * orig_spacing[0]),
-             int(orig_shape[1] / bioxel_size * orig_spacing[1]),
-             int(orig_shape[2] / bioxel_size * orig_spacing[2]))
-
-    return (shape[0] if shape[0] > 0 else 1,
-            shape[1] if shape[1] > 0 else 1,
-            shape[2] if shape[2] > 0 else 1)
-
-
-def get_layer_size(shape: tuple, bioxel_size: float, scale: float = 1.0):
-    size = (float(shape[0] * bioxel_size * scale),
-            float(shape[1] * bioxel_size * scale),
-            float(shape[2] * bioxel_size * scale))
-
-    return size
-
-
-def get_ext(filepath: str) -> str:
-    file_path = Path(filepath)
-    if file_path.name.endswith(".nii.gz"):
-        return ".nii.gz"
-    elif file_path.name.endswith(".img.gz"):
-        return ".img.gz"
-    elif file_path.name.endswith(".gipl.gz"):
-        return ".gipl.gz"
-    else:
-        return file_path.suffix
-
-
-def get_sequence_name(filepath: str) -> str:
-    ext = get_ext(filepath)
-    filename = Path(filepath).name.removesuffix(ext)
-    index: str = get_text_index_str(filename)
-    return filename.removesuffix(index)
-
-
-def get_sequence_index(filepath: str) -> int:
-    ext = get_ext(filepath)
-    filename = Path(filepath).name.removesuffix(ext)
-    index: str = get_text_index_str(filename)
-    return int(index) if index else 0
-
-
-def collect_sequence(filepath: str):
-    file_path = Path(filepath).resolve()
-
-    files = list(file_path.parent.iterdir())
-    files = [f for f in files if f.is_file()
-             and get_ext(file_path) == get_ext(f)
-             and get_sequence_name(file_path) == get_sequence_name(f)]
-
-    files.sort(key=get_sequence_index)
-    sequence = [str(f) for f in files]
-    return sequence
-
-
-def parse_volume_data(filepath: str, series_id=""):
-    ext = get_ext(filepath)
-
-    if ext in DICOM_EXTS:
-        dir_path = Path(filepath).resolve().parent
-        reader = sitk.ImageSeriesReader()
-        reader.MetaDataDictionaryArrayUpdateOn()
-        reader.LoadPrivateTagsOn()
-        series_files = reader.GetGDCMSeriesFileNames(
-            str(dir_path), series_id)
-        reader.SetFileNames(series_files)
-
-        itk_volume = reader.Execute()
-        # for k in reader.GetMetaDataKeys(0):
-        #     v = reader.GetMetaData(0, k)
-        #     print(f'({k}) = = "{v}"')
-        name = dir_path.name
-
-    elif ext in SEQUENCE_EXTS:
-        itk_volume = sitk.ReadImage(filepath)
-        if itk_volume.GetDimension() == 2:
-            sequence = collect_sequence(filepath)
-            itk_volume = sitk.ReadImage(sequence)
-            name = get_sequence_name(filepath)
-        else:
-            itk_volume = sitk.ReadImage(filepath)
-            name = Path(filepath).name.removesuffix(ext)
-    else:
-        itk_volume = sitk.ReadImage(filepath)
-        name = Path(filepath).name.removesuffix(ext)
-
-    # for key in itk_volume.GetMetaDataKeys():
-    #     print(f"{key},{itk_volume.GetMetaData(key)}")
-
-    if itk_volume.GetDimension() == 3:
-        itk_volume = sitk.DICOMOrient(itk_volume, 'RAS')
-
-        meta = {
-            "name": name,
-            "shape": tuple(itk_volume.GetSize()),
-            "spacing": tuple(itk_volume.GetSpacing()),
-            "origin": tuple(itk_volume.GetOrigin()),
-            "direction": tuple(itk_volume.GetDirection()),
-            "is_oriented": True
-        }
-
-        volume = sitk.GetArrayFromImage(itk_volume)
-
-        # transpose ijk to kji
-        if volume.ndim == 4:
-            volume = np.transpose(volume, (2, 1, 0, 3))
-        else:
-            volume = np.transpose(volume)
-            volume = np.expand_dims(volume, axis=-1)
-
-    else:
-        # FIXME: not sure...
-        print(itk_volume.GetDirection())
-        direction = np.array(itk_volume.GetDirection())
-        direction = direction.reshape(3, 3) if itk_volume.GetDimension() == 3 \
-            else direction.reshape(4, 4)
-
-        direction = direction[1:, 1:]
-        direction = tuple(direction.flatten())
-
-        meta = {
-            "name": name,
-            "shape": tuple(itk_volume.GetSize()[:3]),
-            "spacing": tuple(itk_volume.GetSpacing()[:3]),
-            "origin": tuple(itk_volume.GetOrigin()[:3]),
-            "direction": direction,
-            "is_oriented": False
-        }
-
-        volume = sitk.GetArrayFromImage(itk_volume)
-
-        if volume.ndim == 5:
-            volume = np.transpose(volume, (0, 3, 2, 1, 4))
-        else:
-            volume = np.transpose(volume, (0, 3, 2, 1))
-            volume = np.expand_dims(volume, axis=-1)
-
-    return volume, meta
-
-
-class ImportVolumeDataDialog(bpy.types.Operator):
-    bl_idname = "bioxelnodes.import_volume_data_dialog"
-    bl_label = "Volumetric Data as Bioxel Layer"
-    bl_description = "Import Volumetric Data as Bioxel Layer"
-    bl_options = {'UNDO'}
-
-    filepath: bpy.props.StringProperty(
-        subtype="FILE_PATH"
-    )  # type: ignore
-
-    container_name: bpy.props.StringProperty(
-        name="Container Name"
-    )   # type: ignore
-
-    layer_name: bpy.props.StringProperty(
-        name="Layer Name",
-    )   # type: ignore
-
-    series_id: bpy.props.StringProperty()   # type: ignore
-
-    container: bpy.props.StringProperty()   # type: ignore
-
-    read_as: bpy.props.EnumProperty(
-        name="Read as",
-        default="scalar",
-        items=[("scalar", "Scalar", ""),
-               ("label", "Labels", "")]
-    )  # type: ignore
-
-    bioxel_size: bpy.props.FloatProperty(
-        name="Bioxel Size (Larger size means small resolution)",
-        soft_min=0.1, soft_max=10.0,
-        min=0.1, max=1e2,
-        default=1,
-    )  # type: ignore
-
-    orig_spacing: bpy.props.FloatVectorProperty(
-        name="Original Spacing",
-        default=(1, 1, 1),
-    )  # type: ignore
-
-    orig_shape: bpy.props.IntVectorProperty(
-        name="Original Shape",
-        default=(100, 100, 100)
-    )  # type: ignore
-
-    scene_scale: bpy.props.FloatProperty(
-        name="Scene Scale (Bioxel Unit pre Blender Unit)",
-        soft_min=0.0001, soft_max=10.0,
-        min=1e-6, max=1e6,
-        default=0.01,
-    )  # type: ignore
-
-    is_time_sequence: bpy.props.BoolProperty(
-        name="Is Time Sequence",
-        default=False,
-    )  # type: ignore
-
-    split_channels: bpy.props.BoolProperty(
-        name="Split Channels",
-        default=False,
-    )  # type: ignore
-
-    def execute(self, context):
-        is_first_import = len(get_all_layers()) == 0
-        volume, meta = parse_volume_data(self.filepath)
-        container_name = self.container_name or meta['name'] or "Container"
-        bioxel_size = self.bioxel_size
-        orig_spacing = self.orig_spacing
-
-        layer_spacing = (
-            meta['spacing'][0] / orig_spacing[0] * bioxel_size,
-            meta['spacing'][1] / orig_spacing[1] * bioxel_size,
-            meta['spacing'][2] / orig_spacing[2] * bioxel_size
-        )
-
-        dtype_index = volume.dtype.num
-
-        layer_shape = get_layer_shape(
-            bioxel_size, meta['shape'], orig_spacing)
-
-        # 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(meta['origin'])
-        )
-
-        mat_rotation = mathutils.Matrix(
-            np.array(meta['direction']).reshape((3, 3))
-        ).to_4x4()
-
-        mat_scale = mathutils.Matrix.Scale(
-            bioxel_size, 4
-        )
-
-        transfrom = mat_lps2ras @ mat_location @ mat_rotation @ mat_scale \
-            if meta['is_oriented'] else mat_location @ mat_rotation @ mat_scale
-
-        # Wrapper a Container
-        if not self.container:
-            # 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
-            )
-
-            bpy.ops.mesh.primitive_cube_add(
-                enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1)
-            )
-            container = bpy.context.active_object
-
-            bbox_verts = calc_bbox_verts((0, 0, 0), layer_shape)
-            for index, vert in enumerate(container.data.vertices):
-                vert.co = transfrom @ mathutils.Vector(bbox_verts[index])
-
-            container.matrix_world = mat_ras2blender @ mat_scene_scale
-            container.name = container_name
-            container.data.name = container_name
-
-            container['bioxel_container'] = True
-            container['scene_scale'] = scene_scale
-            bpy.ops.node.new_geometry_nodes_modifier()
-            container_node_group = container.modifiers[0].node_group
-            input_node = get_nodes_by_type(container_node_group,
-                                           'NodeGroupInput')[0]
-            container_node_group.links.remove(input_node.outputs[0].links[0])
-
-        else:
-            container = bpy.data.objects[self.container]
-            container_node_group = container.modifiers[0].node_group
-
-        preferences = context.preferences.addons[__package__].preferences
-
-        # TODO: change to transform when 4.2?
-        loc, rot, sca = transfrom.decompose()
-        layer_origin = tuple(loc)
-        layer_rotation = tuple(rot.to_euler())
-
-        def create_layer(volume, layer_name, layer_shape, layer_type="scalar"):
-            if volume.ndim == 4:
-                grids_sequence = []
-                for f in range(volume.shape[0]):
-                    print(f"Resampling...")
-                    frame = ski.resize(volume[f, :, :, :],
-                                       layer_shape,
-                                       preserve_range=True,
-                                       anti_aliasing=volume.dtype.kind != "b")
-
-                    grid = vdb.FloatGrid()
-                    frame = frame.copy().astype(np.float32)
-                    grid.copyFromArray(frame)
-                    grid.transform = vdb.createLinearTransform(
-                        transfrom.transposed())
-                    grid.name = layer_type
-                    grids_sequence.append([grid])
-
-                vdb_paths = save_vdbs(grids_sequence, context)
-
-                # Read VDB
-                print(f"Loading the cache to Blender scene...")
-                files = [{"name": str(vdb_path.name), "name": str(vdb_path.name)}
-                         for vdb_path in vdb_paths]
-
-                bpy.ops.object.volume_import(filepath=str(vdb_paths[0]), directory=str(vdb_paths[0].parent),
-                                             files=files, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-
-            else:
-                volume = ski.resize(volume,
-                                    layer_shape,
-                                    preserve_range=True,
-                                    anti_aliasing=volume.dtype.kind != "b")
-
-                grid = vdb.FloatGrid()
-                volume = volume.copy().astype(np.float32)
-                grid.copyFromArray(volume)
-                grid.transform = vdb.createLinearTransform(
-                    transfrom.transposed())
-                grid.name = layer_type
-
-                vdb_path = save_vdb([grid], context)
-
-                # Read VDB
-                print(f"Loading the cache to Blender scene...")
-                bpy.ops.object.volume_import(filepath=str(vdb_path),
-                                             align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-
-            layer = bpy.context.active_object
-            layer.data.sequence_mode = 'REPEAT'
-
-            # Set props to VDB object
-            layer.name = layer_name
-            layer.data.name = layer_name
-
-            lock_transform(layer)
-            hide_in_ray(layer)
-            layer.hide_select = True
-            layer.hide_render = True
-            layer.hide_viewport = True
-            layer.data.display.use_slice = True
-            layer.data.display.density = 1e-05
-
-            layer['bioxel_layer'] = True
-            layer['bioxel_layer_type'] = layer_type
-            layer.parent = container
-
-            for collection in layer.users_collection:
-                collection.objects.unlink(layer)
-
-            for collection in container.users_collection:
-                collection.objects.link(layer)
-
-            print(f"Creating layer ...")
-
-            bpy.ops.node.new_geometry_nodes_modifier()
-            node_group = layer.modifiers[0].node_group
-
-            input_node = get_nodes_by_type(node_group, 'NodeGroupInput')[0]
-            output_node = get_nodes_by_type(node_group, 'NodeGroupOutput')[0]
-
-            to_layer_node = custom_nodes.add_node(node_group,
-                                                  "BioxelNodes__ConvertToLayer")
-
-            node_group.links.new(input_node.outputs[0],
-                                 to_layer_node.inputs[0])
-            node_group.links.new(to_layer_node.outputs[0],
-                                 output_node.inputs[0])
-
-            # for compatibility to old vdb
-            # to_layer_node.inputs['Not Transfromed'].default_value = True
-            to_layer_node.inputs['Layer ID'].default_value = random.randint(-200000000,
-                                                                            200000000)
-            to_layer_node.inputs['Data Type'].default_value = dtype_index
-            to_layer_node.inputs['Bioxel Size'].default_value = bioxel_size
-            to_layer_node.inputs['Shape'].default_value = layer_shape
-            to_layer_node.inputs['Origin'].default_value = layer_origin
-            to_layer_node.inputs['Rotation'].default_value = layer_rotation
-
-            move_node_between_nodes(to_layer_node, [input_node, output_node])
-
-            return layer
-
-        def create_mask_node(layer, node_type, node_label, offset):
-            mask_node = custom_nodes.add_node(container_node_group,
-                                              node_type)
-            mask_node.label = node_label
-            mask_node.inputs[0].default_value = layer
-
-            # Connect to output if no output linked
-            output_node = get_nodes_by_type(container_node_group,
-                                            'NodeGroupOutput')[0]
-            if len(output_node.inputs[0].links) == 0:
-                container_node_group.links.new(mask_node.outputs[0],
-                                               output_node.inputs[0])
-                move_node_to_node(mask_node, output_node, (-300, 0))
-            else:
-                move_node_to_node(mask_node, output_node, offset)
-
-        # change shape as sequence or not
-        if self.is_time_sequence:
-            # 4->5 or 5->5
-            if volume.ndim == 4:
-                # channel as frame
-                volume = volume.transpose(3, 0, 1, 2)
-                volume = np.expand_dims(volume, axis=-1)
-
-        else:
-            # 4->4 or 5->4
-            if volume.ndim == 5:
-                # select frame 0
-                volume = volume[0, :, :, :, :]
-
-        if self.read_as == "label":
-            layer_name = self.layer_name or "Label"
-            volume = np.amax(volume, -1)
-            volume = volume.astype(int)
-            orig_max = int(np.max(volume))
-            orig_min = int(np.min(volume))
-
-            for i in range(orig_max):
-                label = volume == np.full_like(volume, i+1)
-                layer_name_i = f"{layer_name}_{i+1}"
-
-                layer = create_layer(volume=label,
-                                     layer_name=f"{container_name}_{layer_name_i}",
-                                     layer_shape=layer_shape,
-                                     layer_type="label")
-
-                mask_node = create_mask_node(layer=layer,
-                                             node_type='BioxelNodes_MaskByLabel',
-                                             node_label=layer_name_i,
-                                             offset=(0, -100 * (i+1)))
-
-        else:
-            layer_name = self.layer_name or "Scalar"
-            # SHOULD NOT change any value!
-            volume = volume.astype(np.float32)
-
-            if self.split_channels:
-                for i in range(volume.shape[-1]):
-                    scalar = volume[:, :, :, :,
-                                    0] if self.is_time_sequence else volume[:, :, :, i]
-                    orig_max = float(np.max(scalar))
-                    orig_min = float(np.min(scalar))
-
-                    scalar_offset = 0
-                    if orig_min < 0:
-                        scalar_offset = -orig_min
-                        scalar = scalar + np.full_like(scalar, scalar_offset)
-
-                    layer_name_i = f"{layer_name}_{i+1}"
-                    layer = create_layer(volume=scalar,
-                                         layer_name=f"{container_name}_{layer_name_i}",
-                                         layer_shape=layer_shape,
-                                         layer_type="scalar")
-
-                    layer_node_group = layer.modifiers[0].node_group
-                    to_layer_node = layer_node_group.nodes['BioxelNodes__ConvertToLayer']
-                    to_layer_node.inputs['Scalar Offset'].default_value = scalar_offset
-                    to_layer_node.inputs['Scalar Max'].default_value = orig_max
-                    to_layer_node.inputs['Scalar Min'].default_value = orig_min
-
-                    mask_node = create_mask_node(layer=layer,
-                                                 node_type='BioxelNodes_MaskByThreshold',
-                                                 node_label=layer_name_i,
-                                                 offset=(0, -100 * (i+1)))
-
-            else:
-                volume = np.amax(volume, -1)
-                orig_max = float(np.max(volume))
-                orig_min = float(np.min(volume))
-
-                scalar_offset = 0
-                if orig_min < 0:
-                    scalar_offset = -orig_min
-                    volume = volume + np.full_like(volume, scalar_offset)
-
-                layer = create_layer(volume=volume,
-                                     layer_name=f"{container_name}_{layer_name}",
-                                     layer_shape=layer_shape,
-                                     layer_type="scalar")
-
-                layer_node_group = layer.modifiers[0].node_group
-                to_layer_node = layer_node_group.nodes['BioxelNodes__ConvertToLayer']
-                to_layer_node.inputs['Scalar Offset'].default_value = scalar_offset
-                to_layer_node.inputs['Scalar Max'].default_value = orig_max
-                to_layer_node.inputs['Scalar Min'].default_value = orig_min
-
-                mask_node = create_mask_node(layer=layer,
-                                             node_type='BioxelNodes_MaskByThreshold',
-                                             node_label=layer_name,
-                                             offset=(0, -100))
-
-        select_object(container)
-
-        # Change render setting for better result
-        if preferences.do_change_render_setting and is_first_import:
-            bpy.context.scene.render.engine = 'CYCLES'
-            try:
-                bpy.context.scene.cycles.shading_system = True
-                bpy.context.scene.cycles.volume_bounces = 12
-                bpy.context.scene.cycles.transparent_max_bounces = 16
-                bpy.context.scene.cycles.volume_preview_step_rate = 10
-                bpy.context.scene.cycles.volume_step_rate = 10
-                bpy.context.scene.eevee.volumetric_tile_size = '2'
-                bpy.context.scene.eevee.volumetric_shadow_samples = 128
-                bpy.context.scene.eevee.volumetric_samples = 256
-            except:
-                pass
-
-        self.report({"INFO"}, "Successfully Imported")
-
-        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        if self.read_as == "label":
-            volume_dtype = "Label"
-        elif self.read_as == "scalar":
-            volume_dtype = "Scalar"
-        title = f"Import as **{volume_dtype}** (Add to Container: {self.container})" \
-            if self.container != "" else f"Import as **{volume_dtype}** (Init a Container)"
-        context.window_manager.invoke_props_dialog(self,
-                                                   width=500,
-                                                   title=title)
-        return {'RUNNING_MODAL'}
-
-    def draw(self, context):
-        layer_shape = get_layer_shape(self.bioxel_size,
-                                      self.orig_shape,
-                                      self.orig_spacing)
-        layer_size = get_layer_size(layer_shape,
-                                    self.bioxel_size,
-                                    self.scene_scale)
-
-        bioxel_count = layer_shape[0] * layer_shape[1] * layer_shape[2]
-        layer_shape_text = f"Shape will be: {str(layer_shape)} {bioxel_count:,} "
-        if bioxel_count > 100000000:
-            layer_shape_text += "**TOO LARGE!**"
-
-        layer_size_text = f"Size will be: ({layer_size[0]:.2f}, {layer_size[1]:.2f}, {layer_size[2]:.2f}) m"
-
-        layout = self.layout
-        if self.container == "":
-            layout.prop(self, "container_name")
-        layout.prop(self, "layer_name")
-
-        panel = layout.box()
-        panel.prop(self, "bioxel_size")
-        row = panel.row()
-        row.prop(self, "orig_spacing")
-        panel.label(text=layer_shape_text)
-
-        panel = layout.box()
-        panel.prop(self, "is_time_sequence")
-        if self.read_as == "scalar":
-            panel.prop(self, "split_channels")
-
-        if self.container == "":
-            panel = layout.box()
-            panel.prop(self, "scene_scale")
-            panel.label(text=layer_size_text)
-
-
-def get_series_ids(self, context):
-    items = []
-    for index, series_id in enumerate(self.series_ids):
-        items.append((
-            series_id.id,
-            series_id.label,
-            "",
-            index
-        ))
-
-    return items
-
-
-class ParseVolumeData(bpy.types.Operator):
-    bl_idname = "bioxelnodes.parse_volume_data"
-    bl_label = "Volumetric Data as Bioxel Layer"
-    bl_description = "Import Volumetric Data as Bioxel Layer"
-    bl_options = {'UNDO'}
-
-    filepath: bpy.props.StringProperty(subtype="FILE_PATH")  # type: ignore
-    directory: bpy.props.StringProperty(subtype='DIR_PATH')  # type: ignore
-    container: bpy.props.StringProperty()   # type: ignore
-
-    read_as: bpy.props.EnumProperty(
-        name="Read as",
-        default="scalar",
-        items=[("scalar", "Scalar", ""),
-               ("label", "Labels", "")]
-    )  # type: ignore
-
-    series_id: bpy.props.EnumProperty(
-        name="Select Series",
-        items=get_series_ids
-    )  # type: ignore
-
-    series_ids: bpy.props.CollectionProperty(
-        type=BIOXELNODES_Series)  # type: ignore
-
-    def execute(self, context):
-        ext = get_ext(self.filepath)
-        if ext not in SUPPORT_EXTS:
-            self.report({"WARNING"}, "Not supported extension.")
-            return {'CANCELLED'}
-
-        print("Collecting Meta Data...")
-        volume, meta = parse_volume_data(self.filepath)
-
-        for key, value in meta.items():
-            print(f"{key}: {value}")
-
-        if self.read_as == "label":
-            not_int = volume.dtype.kind != "b" and volume.dtype.kind != "i" and volume.dtype.kind != "u"
-            too_large = np.max(volume) > 100
-
-            if not_int or too_large:
-                self.report(
-                    {"WARNING"}, "This volume data does not looks like label, please check again.")
-                return {'CANCELLED'}
-
-        # do_orient = ext not in SEQUENCE_EXTS or ext in DICOM_EXTS
-
-        orig_shape = meta['shape']
-        orig_spacing = meta['spacing']
-        min_size = min(orig_spacing[0], orig_spacing[1], orig_spacing[2])
-        bioxel_size = max(min_size, 1.0)
-
-        layer_size = get_layer_size(orig_shape,
-                                    bioxel_size)
-        log10 = math.floor(math.log10(max(*layer_size)))
-        scene_scale = math.pow(10, -log10)
-
-        if self.container:
-            container = bpy.data.objects[self.container]
-            container_name = container.name
-        else:
-            container_name = meta['name']
-
-        bpy.ops.bioxelnodes.import_volume_data_dialog(
-            'INVOKE_DEFAULT',
-            filepath=self.filepath,
-            container_name=container_name,
-            orig_shape=orig_shape,
-            orig_spacing=orig_spacing,
-            bioxel_size=bioxel_size,
-            series_id=self.series_id or "",
-            # do_orient=do_orient,
-            container=self.container,
-            read_as=self.read_as,
-            scene_scale=scene_scale
-        )
-
-        self.report({"INFO"}, "Successfully Readed.")
-
-        return {'FINISHED'}
-
-    def modal(self, context, event):
-        self.execute(context)
-        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        if not self.filepath and not self.directory:
-            return {'CANCELLED'}
-
-        show_message('Parsing volume data, it may take a while...',
-                     'Please be patient...')
-
-        if get_ext(self.filepath) == '.dcm':
-            dir_path = Path(self.filepath).parent
-            reader = sitk.ImageSeriesReader()
-            reader.MetaDataDictionaryArrayUpdateOn()
-            reader.LoadPrivateTagsOn()
-            series_ids = reader.GetGDCMSeriesIDs(str(dir_path))
-
-            for _id in series_ids:
-                series_id = self.series_ids.add()
-                series_id.id = _id
-                series_id.label = _id
-
-            if len(series_ids) > 1:
-                context.window_manager.invoke_props_dialog(self, width=400)
-                return {'RUNNING_MODAL'}
-            else:
-                self.series_id = series_ids[0]
-
-        context.window_manager.modal_handler_add(self)
-        return {'RUNNING_MODAL'}
-
-    def draw(self, context):
-        layout = self.layout
-        layout.prop(self, "series_id")
-        layout.label(
-            text="Reading image data, it may take a while...")
-        layout.label(
-            text="Please be patient...")
-
-
-class ImportVolumeData():
-    bl_options = {'UNDO'}
-
-    filepath: bpy.props.StringProperty(subtype="FILE_PATH")  # type: ignore
-    directory: bpy.props.StringProperty(subtype='DIR_PATH')  # type: ignore
-
-    read_as = "scalar"
-
-    def execute(self, context):
-        containers = get_container_from_selection()
-
-        if len(containers) > 0:
-            bpy.ops.bioxelnodes.parse_volume_data(
-                'INVOKE_DEFAULT',
-                filepath=self.filepath,
-                directory=self.directory,
-                container=containers[0].name,
-                read_as=self.read_as
-            )
-        else:
-            bpy.ops.bioxelnodes.parse_volume_data(
-                'INVOKE_DEFAULT',
-                filepath=self.filepath,
-                directory=self.directory,
-                read_as=self.read_as
-            )
-
-        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        context.window_manager.fileselect_add(self)
-        return {'RUNNING_MODAL'}
-
-
-class ImportAsScalarLayer(bpy.types.Operator, ImportVolumeData):
-    bl_idname = "bioxelnodes.import_as_scalar_layer"
-    bl_label = "Import as Scalar"
-    bl_description = "Import Volumetric Data to Container as Scalar"
-    read_as = "scalar"
-
-
-class ImportAsLabelLayer(bpy.types.Operator, ImportVolumeData):
-    bl_idname = "bioxelnodes.import_as_label_layer"
-    bl_label = "Import as Label"
-    bl_description = "Import Volumetric Data to Container as Label"
-    read_as = "label"
-
-
-try:
-    class BIOXELNODES_FH_ImportVolumeData(bpy.types.FileHandler):
-        bl_idname = "BIOXELNODES_FH_ImportVolumeData"
-        bl_label = "File handler for dicom import"
-        bl_import_operator = "bioxelnodes.parse_volume_data"
-        bl_file_extensions = ";".join(FH_EXTS)
-
-        @classmethod
-        def poll_drop(cls, context):
-            return (context.area and context.area.type == 'VIEW_3D')
-except:
-    ...
-
-
-class ExportVolumeData(bpy.types.Operator):
-    bl_idname = "bioxelnodes.export_volume_data"
-    bl_label = "Export Layer as VDB"
-    bl_description = "Export Layer as VDB"
-    bl_options = {'UNDO'}
-
-    filepath: bpy.props.StringProperty(
-        subtype="FILE_PATH"
-    )  # type: ignore
-
-    filename_ext = ".vdb"
-
-    @classmethod
-    def poll(cls, context):
-        layer = get_layer(bpy.context.active_object)
-        return True if layer else False
-
-    def invoke(self, context, event):
-        context.window_manager.fileselect_add(self)
-        return {'RUNNING_MODAL'}
-
-    def execute(self, context):
-        layer = get_layer(bpy.context.active_object)
-
-        filepath = f"{self.filepath.split('.')[0]}.vdb"
-        # "//"
-        source_dir = bpy.path.abspath(layer.data.filepath)
-
-        output_path: Path = Path(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/io_points.py

@@ -1,25 +0,0 @@
-# TODO: WIP
-import bpy
-import bmesh
-
-
-def create_points_obj(points, name="points"):
-    bpy.ops.mesh.primitive_cube_add(
-        enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1)
-    )
-    obj = bpy.context.active_object
-    mesh = obj.data
-
-    bm = bmesh.new()
-    value_layer = bm.verts.layers.float.new('value')
-
-    for point in points:
-        pos = point['pos']
-        value = point['value']
-        vert = bm.verts.new(pos)  # add a new vert
-        vert[value_layer] = value
-
-    # make the bmesh the object's mesh
-    bm.to_mesh(mesh)
-    bm.free()  # always do this when finished
-    return obj

bioxelnodes/menus.py

@@ -1,10 +1,21 @@
 import bpy
 
-from .utils import get_container_from_selection
+from .bioxelutils.container import get_container_objs_from_selection
-from .operators import (AddPieCutter, AddPlaneCutter, AddCylinderCutter, AddCubeCutter, AddSphereCutter, CombineLabels,
+from .operators.layer import (CombineLabels, SignScalar,
-                        ConvertToMesh, InvertScalar, FillByLabel, FillByThreshold, FillByRange, PickBboxWire, PickMesh, PickVolume)
+                              FillByLabel, FillByThreshold, FillByRange)
-from .io import ExportVolumeData, ImportAsLabelLayer, ImportAsScalarLayer
+from .operators.container import (SaveContainer, LoadContainer,
-from .save import CleanAllCaches, ReLinkNodes, SaveLayers, SaveStagedData
+                                  AddPieCutter, AddPlaneCutter,
+                                  AddCylinderCutter, AddCubeCutter, AddSphereCutter,
+                                  PickBboxWire, PickMesh, PickVolume)
+from .operators.io import (ExportVolumetricData,
+                           ImportAsLabelLayer, ImportAsScalarLayer)
+from .operators.misc import (CleanAllCaches,
+                             ReLinkNodes, SaveCaches, SaveStagedData)
+
+
+def container_is_selected():
+    container_objs = get_container_objs_from_selection()
+    return len(container_objs) > 0
 
 
 class PickFromContainerMenu(bpy.types.Menu):
@@ -24,7 +35,7 @@ class ModifyLayerMenu(bpy.types.Menu):
 
     def draw(self, context):
         layout = self.layout
-        layout.operator(InvertScalar.bl_idname)
+        layout.operator(SignScalar.bl_idname)
         layout.operator(FillByThreshold.bl_idname)
         layout.operator(FillByRange.bl_idname)
         layout.operator(FillByLabel.bl_idname)
@@ -60,8 +71,7 @@ class BioxelNodesView3DMenu(bpy.types.Menu):
 
     def draw(self, context):
         layout = self.layout
-        containers = get_container_from_selection()
+        is_selected = container_is_selected()
-        is_selected = len(containers) > 0
         layout.operator(ImportAsScalarLayer.bl_idname,
                         text=ImportAsScalarLayer.bl_label+" (Add to)"
                         if is_selected else ImportAsScalarLayer.bl_label+" (Init)")
@@ -79,7 +89,7 @@ class BioxelNodesView3DMenu(bpy.types.Menu):
         layout.operator(PickVolume.bl_idname)
         layout.operator(PickBboxWire.bl_idname)
         layout.separator()
-        layout.operator(SaveLayers.bl_idname)
+        layout.operator(SaveCaches.bl_idname)
 
 
 class BioxelNodesOutlinerMenu(bpy.types.Menu):
@@ -88,8 +98,7 @@ class BioxelNodesOutlinerMenu(bpy.types.Menu):
 
     def draw(self, context):
         layout = self.layout
-        containers = get_container_from_selection()
+        is_selected = container_is_selected()
-        is_selected = len(containers) > 0
         layout.operator(ImportAsScalarLayer.bl_idname,
                         text=ImportAsScalarLayer.bl_label+" (Add to)"
                         if is_selected else ImportAsScalarLayer.bl_label+" (Init)")
@@ -107,21 +116,18 @@ class BioxelNodesOutlinerMenu(bpy.types.Menu):
         layout.operator(PickVolume.bl_idname)
         layout.operator(PickBboxWire.bl_idname)
         layout.separator()
-        layout.operator(SaveLayers.bl_idname)
+        layout.operator(SaveCaches.bl_idname)
         layout.separator()
-        layout.operator(InvertScalar.bl_idname)
+        layout.operator(SignScalar.bl_idname)
         layout.operator(FillByThreshold.bl_idname)
         layout.operator(FillByRange.bl_idname)
         layout.operator(FillByLabel.bl_idname)
         layout.operator(CombineLabels.bl_idname)
-        layout.separator()
-        layout.operator(ExportVolumeData.bl_idname)
 
 
 def TOPBAR_FILE_IMPORT(self, context):
     layout = self.layout
-    containers = get_container_from_selection()
+    is_selected = container_is_selected()
-    is_selected = len(containers) > 0
 
     layout.separator()
     layout.menu(ImportLayerMenu.bl_idname, text="Volumetric Data as Bioxel (Add to)"
@@ -131,7 +137,7 @@ def TOPBAR_FILE_IMPORT(self, context):
 def TOPBAR_FILE_EXPORT(self, context):
     layout = self.layout
     layout.separator()
-    layout.operator(ExportVolumeData.bl_idname,
+    layout.operator(ExportVolumetricData.bl_idname,
                     text="Bioxel Layer (.vdb)")
 
 
@@ -153,12 +159,14 @@ class BioxelNodesTopbarMenu(bpy.types.Menu):
 
     def draw(self, context):
         layout = self.layout
-        containers = get_container_from_selection()
+        is_selected = container_is_selected()
-        is_selected = len(containers) > 0
 
         layout.menu(ImportLayerMenu.bl_idname, text=ImportLayerMenu.bl_label+" (Add to)"
                     if is_selected else ImportLayerMenu.bl_label+" (Init)")
         layout.separator()
+        layout.operator(LoadContainer.bl_idname)
+        layout.operator(SaveContainer.bl_idname)
+        layout.separator()
         layout.menu(AddCutterMenu.bl_idname)
         layout.menu(PickFromContainerMenu.bl_idname)
         layout.separator()
@@ -175,7 +183,7 @@ def TOPBAR(self, context):
 
 def add():
     bpy.types.TOPBAR_MT_file_import.append(TOPBAR_FILE_IMPORT)
-    bpy.types.TOPBAR_MT_file_export.append(TOPBAR_FILE_EXPORT)
+    # bpy.types.TOPBAR_MT_file_export.append(TOPBAR_FILE_EXPORT)
     bpy.types.OUTLINER_MT_object.append(OUTLINER_OBJECT)
     bpy.types.VIEW3D_MT_object_context_menu.append(VIEW3D_OBJECT)
     bpy.types.TOPBAR_MT_editor_menus.append(TOPBAR)
@@ -183,7 +191,7 @@ def add():
 
 def remove():
     bpy.types.TOPBAR_MT_file_import.remove(TOPBAR_FILE_IMPORT)
-    bpy.types.TOPBAR_MT_file_export.remove(TOPBAR_FILE_EXPORT)
+    # bpy.types.TOPBAR_MT_file_export.remove(TOPBAR_FILE_EXPORT)
     bpy.types.OUTLINER_MT_object.remove(OUTLINER_OBJECT)
     bpy.types.VIEW3D_MT_object_context_menu.remove(VIEW3D_OBJECT)
     bpy.types.TOPBAR_MT_editor_menus.remove(TOPBAR)

bioxelnodes/nodes.py

@@ -1,62 +1,8 @@
 
 from pathlib import Path
 from .customnodes import CustomNodes
-import bpy
 
-# def set_object_to_node_factory(object_type:str):
+NODE_FILE = "BioxelNodes_4.2"
-#     if object_type == "plane":
-#         create_object = """
-#     bpy.ops.mesh.primitive_plane_add(size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-#         """
-#     callback_str = f"""
-# import bpy
-# from ..utils import get_container
-# container = get_container(bpy.context.active_object)
-# if container:
-#     {create_object}
-#     object = bpy.context.active_object
-#     node.inputs[0].default_value = object
-# else:
-#     print('Cannot find any Bioxel Container.')
-#     """
-#     return callback_str
-
-
-# def add_driver_to_node_factory(source_prop, target_prop):
-#     callback_str = f"""
-# import bpy
-# 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
-#     add_direct_driver(
-#         target=node,
-#         target_prop='{target_prop}',
-#         source=container_obj,
-#         source_prop='{source_prop}'
-#     )
-# else:
-#     print('Cannot find any bioxels.')
-#     """
-#     return callback_str
-
-
-# def set_prop_to_node_factory(source_prop, target_prop):
-#     callback_str = f"""
-# import bpy
-# from .utils import get_bioxels_obj
-# bioxels_obj = get_bioxels_obj(bpy.context.active_object)
-# if bioxels_obj:
-#     container_obj = bioxels_obj.parent
-#     node.inputs.get('{target_prop}').default_value = container_obj.get(
-#         '{source_prop}')
-# else:
-#     print('Cannot find any bioxels.')
-#     """
-#     return callback_str
-
-
-NODE_FILE = "BioxelNodes_4.1"
 
 MENU_ITEMS = [
     {

bioxelnodes/operators.py

@@ -1,929 +0,0 @@
-from pathlib import Path
-import random
-import bpy
-import pyopenvdb as vdb
-import numpy as np
-import bmesh
-from . import skimage as ski
-from . import scipy
-from .nodes import custom_nodes
-from .utils import (get_container, get_container_from_selection, get_container_layers,
-                    get_layer, get_nodes_by_type, hide_in_ray, lock_transform, move_node_between_nodes, move_node_to_node, save_vdb, select_object)
-
-
-def get_layer_name(layer):
-    container = layer.parent
-    return layer.name.removeprefix(container.name).replace("_", "")
-
-
-def get_grids(layer):
-    layer_dir = bpy.path.abspath(layer.data.filepath)
-    grids, base_metadata = vdb.readAll(layer_dir)
-    return grids
-
-
-def set_volume(grids, index, volume):
-    grids[index].clear()
-    grids[index].copyFromArray(volume.copy().astype(np.float32))
-
-
-def get_volume(grids, index, shape):
-    volume = np.ndarray(shape, np.float32)
-    volume.fill(index)
-    grids[0].copyToArray(volume)
-    return volume
-
-
-def get_shape(layer):
-    layer_node = layer.modifiers[0].node_group.nodes['BioxelNodes__ConvertToLayer']
-    return [int(a)
-            for a in layer_node.inputs['Shape'].default_value]
-
-
-def get_layer_meta(layer, key: str):
-    layer_node = layer.modifiers[0].node_group.nodes['BioxelNodes__ConvertToLayer']
-    return layer_node.inputs[key].default_value
-
-
-def set_layer_meta(layer, key: str, value):
-    layer_node = layer.modifiers[0].node_group.nodes['BioxelNodes__ConvertToLayer']
-    layer_node.inputs[key].default_value = value
-
-
-def add_mask_node(container, layer, node_type: str, node_label: str):
-    modifier = container.modifiers[0]
-    container_node_group = modifier.node_group
-
-    mask_node = custom_nodes.add_node(container_node_group, node_type)
-    mask_node.label = node_label
-    mask_node.inputs[0].default_value = layer
-
-    # Connect to output if no output linked
-    output_node = get_nodes_by_type(container_node_group,
-                                    'NodeGroupOutput')[0]
-
-    if len(output_node.inputs[0].links) == 0:
-        container_node_group.links.new(mask_node.outputs[0],
-                                       output_node.inputs[0])
-        move_node_to_node(mask_node, output_node, (-300, 0))
-    else:
-        move_node_to_node(mask_node, output_node, (0, -100))
-
-    return mask_node
-
-
-def deep_copy_layer(vdb_path, base_layer, name):
-    # Read VDB
-    print(f"Loading the cache to Blender scene...")
-    bpy.ops.object.volume_import(
-        filepath=str(vdb_path), align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-
-    copyed_layer = bpy.context.active_object
-
-    # Set props to VDB object
-    copyed_layer.name = name
-    copyed_layer.data.name = name
-
-    lock_transform(copyed_layer)
-    hide_in_ray(copyed_layer)
-    copyed_layer.hide_select = True
-    copyed_layer.hide_render = True
-    copyed_layer.hide_viewport = True
-    copyed_layer.data.display.use_slice = True
-    copyed_layer.data.display.density = 1e-05
-
-    copyed_layer['bioxel_layer'] = True
-    copyed_layer['bioxel_layer_type'] = base_layer['bioxel_layer_type']
-    copyed_layer.parent = base_layer.parent
-
-    for collection in copyed_layer.users_collection:
-        collection.objects.unlink(copyed_layer)
-
-    for collection in base_layer.users_collection:
-        collection.objects.link(copyed_layer)
-
-    # add convert to layer node
-    base_layer_node = base_layer.modifiers[0].node_group.nodes['BioxelNodes__ConvertToLayer']
-
-    not_transformed = base_layer_node.inputs['Not Transfromed'].default_value
-    dtype_index = base_layer_node.inputs['Data Type'].default_value
-    bioxel_size = base_layer_node.inputs['Bioxel Size'].default_value
-    layer_shape = base_layer_node.inputs['Shape'].default_value
-    layer_origin = base_layer_node.inputs['Origin'].default_value
-    layer_rotation = base_layer_node.inputs['Rotation'].default_value
-    scalar_offset = base_layer_node.inputs['Scalar Offset'].default_value
-    scalar_min = base_layer_node.inputs['Scalar Min'].default_value
-    scalar_max = base_layer_node.inputs['Scalar Max'].default_value
-
-    bpy.ops.node.new_geometry_nodes_modifier()
-    node_group = copyed_layer.modifiers[0].node_group
-
-    input_node = get_nodes_by_type(node_group, 'NodeGroupInput')[0]
-    output_node = get_nodes_by_type(node_group, 'NodeGroupOutput')[0]
-
-    copyed_layer_node = custom_nodes.add_node(node_group,
-                                              "BioxelNodes__ConvertToLayer")
-
-    node_group.links.new(input_node.outputs[0], copyed_layer_node.inputs[0])
-    node_group.links.new(copyed_layer_node.outputs[0], output_node.inputs[0])
-
-    # for compatibility to old vdb
-    copyed_layer_node.inputs['Not Transfromed'].default_value = not_transformed
-    copyed_layer_node.inputs['Layer ID'].default_value = random.randint(-200000000,
-                                                                        200000000)
-    copyed_layer_node.inputs['Data Type'].default_value = dtype_index
-    copyed_layer_node.inputs['Bioxel Size'].default_value = bioxel_size
-    copyed_layer_node.inputs['Shape'].default_value = layer_shape
-    copyed_layer_node.inputs['Origin'].default_value = layer_origin
-    copyed_layer_node.inputs['Rotation'].default_value = layer_rotation
-    copyed_layer_node.inputs['Scalar Offset'].default_value = scalar_offset
-    copyed_layer_node.inputs['Scalar Min'].default_value = scalar_min
-    copyed_layer_node.inputs['Scalar Max'].default_value = scalar_max
-
-    return copyed_layer
-
-
-def get_scalar_layer_selection(self, context):
-    items = [("None", "None", "")]
-    container = get_container(bpy.context.active_object)
-    for layer in get_container_layers(container):
-        if layer.get("bioxel_layer_type") == "scalar":
-            items.append((
-                layer.name,
-                layer.name,
-                ""
-            ))
-
-    return items
-
-
-def get_label_layer_selection(self, context):
-    items = [("None", "None", "")]
-    container = get_container(bpy.context.active_object)
-    for layer in get_container_layers(container):
-        if layer.get("bioxel_layer_type") == "label":
-            items.append((
-                layer.name,
-                layer.name,
-                ""
-            ))
-
-    return items
-
-
-# class JoinLayers(bpy.types.Operator):
-#     bl_idname = "bioxelnodes.join_layers"
-#     bl_label = "Join Bioxel Layers"
-#     bl_description = "Join Additional Bioxel Layers"
-#     bl_options = {'UNDO'}
-
-#     base_layer: bpy.props.StringProperty(
-#         options={"HIDDEN"}
-#     )   # type: ignore
-
-#     scalar_layer: bpy.props.EnumProperty(
-#         name="Scalar Layer",
-#         items=get_scalar_layer_selection
-#     )  # type: ignore
-
-#     label_layer: bpy.props.EnumProperty(
-#         name="Label Layer",
-#         items=get_label_layer_selection
-#     )  # type: ignore
-#     # color_layer: bpy.props.StringProperty()   # type: ignore
-
-#     @classmethod
-#     def poll(cls, context):
-#         layer = get_layer(bpy.context.active_object)
-#         return True if layer else False
-
-#     def execute(self, context):
-#         base_layer = bpy.data.objects[self.base_layer]
-
-#         if not base_layer:
-#             self.report({"WARNING"}, "Cannot find any bioxel layer as base.")
-#             return {'FINISHED'}
-
-#         base_layer_dir = bpy.path.abspath(base_layer.data.filepath)
-#         base_grids, base_metadata = vdb.readAll(base_layer_dir)
-
-#         layers = []
-#         if self.scalar_layer != "None":
-#             scalar_layer = bpy.data.objects[self.scalar_layer]
-#             layers.append(scalar_layer)
-
-#         if self.label_layer != "None":
-#             label_layer = bpy.data.objects[self.label_layer]
-#             layers.append(label_layer)
-
-#         # TODO: add color and vector
-
-#         if len(layers) == 0:
-#             self.report({"WARNING"}, "No additinal layers setted.")
-#             return {'FINISHED'}
-
-#         for layer in layers:
-#             layer_dir = bpy.path.abspath(layer.data.filepath)
-#             grids, metadata = vdb.readAll(layer_dir)
-#             base_grids.extend(grids)
-
-#         vdb_path = save_vdb(base_grids, context)
-
-#         joined_layer = deep_copy_layer(vdb_path,
-#                                        base_layer,
-#                                        f"{base_layer.name}_Joined")
-
-#         return {'FINISHED'}
-
-#     def invoke(self, context, event):
-#         base_layer = get_layer(bpy.context.active_object)
-#         self.base_layer = base_layer.name
-#         context.window_manager.invoke_props_dialog(self, width=400)
-#         return {'RUNNING_MODAL'}
-
-
-class InvertScalar(bpy.types.Operator):
-    bl_idname = "bioxelnodes.invert_scalar"
-    bl_label = "Invert Scalar"
-    bl_description = "Invert the scalar value"
-    bl_options = {'UNDO'}
-
-    @classmethod
-    def poll(cls, context):
-        layer = get_layer(bpy.context.active_object)
-        if layer:
-            return layer.get("bioxel_layer_type") == "scalar"
-        else:
-            return False
-
-    def execute(self, context):
-        base_layer = get_layer(bpy.context.active_object)
-
-        container = base_layer.parent
-        inverted_layer_name = f"{get_layer_name(base_layer)}_Inverted"
-
-        base_shape = get_shape(base_layer)
-        scalar_offset = get_layer_meta(base_layer, "Scalar Offset")
-
-        base_grids = get_grids(base_layer)
-        base_volume = get_volume(base_grids, 0, base_shape)
-
-        base_volume = -(base_volume - scalar_offset)
-
-        base_min = float(np.min(base_volume))
-        base_max = float(np.max(base_volume))
-
-        scalar_offset = 0
-        if base_min < 0:
-            scalar_offset = -base_min
-            base_volume = base_volume + scalar_offset
-
-        set_volume(base_grids, 0, base_volume)
-        vdb_path = save_vdb(base_grids, context)
-        inverted_layer = deep_copy_layer(vdb_path,
-                                         base_layer,
-                                         f"{container.name}_{inverted_layer_name}")
-        set_layer_meta(inverted_layer, 'Scalar Offset', scalar_offset)
-        set_layer_meta(inverted_layer, 'Scalar Min', base_min)
-        set_layer_meta(inverted_layer, 'Scalar Max', base_max)
-
-        add_mask_node(container,
-                      inverted_layer,
-                      "BioxelNodes_MaskByThreshold",
-                      inverted_layer_name)
-
-        select_object(container)
-
-        return {'FINISHED'}
-
-
-class FillByThreshold(bpy.types.Operator):
-    bl_idname = "bioxelnodes.fill_by_threshold"
-    bl_label = "Fill Value by Threshold"
-    bl_description = "Fill Value by Threshold"
-    bl_options = {'UNDO'}
-
-    threshold: bpy.props.FloatProperty(
-        name="Threshold",
-        soft_min=0, soft_max=1024,
-        default=128,
-    )  # type: ignore
-
-    fill_value: bpy.props.FloatProperty(
-        name="Fill Value",
-        soft_min=0, soft_max=1024.0,
-        default=0,
-    )  # type: ignore
-
-    invert: bpy.props.BoolProperty(
-        name="Invert Area",
-        default=True,
-    )  # type: ignore
-
-    @classmethod
-    def poll(cls, context):
-        layer = get_layer(bpy.context.active_object)
-        if layer:
-            return layer.get("bioxel_layer_type") == "scalar"
-        else:
-            return False
-
-    def execute(self, context):
-        base_layer = get_layer(bpy.context.active_object)
-
-        container = base_layer.parent
-        filled_layer_name = f"{get_layer_name(base_layer)}_{self.threshold}-Filled"
-        scalar_offset = get_layer_meta(base_layer, "Scalar Offset")
-        base_shape = get_shape(base_layer)
-
-        base_grids = get_grids(base_layer)
-        base_volume = get_volume(base_grids, 0, base_shape)
-        mask = base_volume > (self.threshold + scalar_offset)
-        mask = scipy.median_filter(mask.astype(np.float32), size=2)
-        if self.invert:
-            base_volume = mask * base_volume + \
-                (1-mask) * (self.fill_value + scalar_offset)
-        else:
-            base_volume = (1-mask) * base_volume + \
-                mask * (self.fill_value + scalar_offset)
-
-        set_volume(base_grids, 0, base_volume)
-        vdb_path = save_vdb(base_grids, context)
-        filled_layer = deep_copy_layer(vdb_path,
-                                       base_layer,
-                                       f"{container.name}_{filled_layer_name}")
-        mask_node = add_mask_node(container,
-                                  filled_layer,
-                                  "BioxelNodes_MaskByThreshold",
-                                  filled_layer_name)
-
-        mask_node.inputs[1].default_value = self.threshold
-
-        select_object(container)
-
-        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        base_layer = get_layer(bpy.context.active_object)
-        scalar_min = get_layer_meta(base_layer, "Scalar Min")
-        self.fill_value = scalar_min
-        context.window_manager.invoke_props_dialog(self, width=400)
-        return {'RUNNING_MODAL'}
-
-
-class FillByRange(bpy.types.Operator):
-    bl_idname = "bioxelnodes.fill_by_range"
-    bl_label = "Fill Value by Range"
-    bl_description = "Fill Value by Range"
-    bl_options = {'UNDO'}
-
-    from_min: bpy.props.FloatProperty(
-        name="From Min",
-        soft_min=0, soft_max=1024,
-        default=128,
-    )  # type: ignore
-
-    from_max: bpy.props.FloatProperty(
-        name="From Max",
-        soft_min=0, soft_max=1024,
-        default=256,
-    )  # type: ignore
-
-    fill_value: bpy.props.FloatProperty(
-        name="Fill Value",
-        soft_min=0, soft_max=1024.0,
-        default=0,
-    )  # type: ignore
-
-    invert: bpy.props.BoolProperty(
-        name="Invert Area",
-        default=True,
-    )  # type: ignore
-
-    @classmethod
-    def poll(cls, context):
-        layer = get_layer(bpy.context.active_object)
-        if layer:
-            return layer.get("bioxel_layer_type") == "scalar"
-        else:
-            return False
-
-    def execute(self, context):
-        base_layer = get_layer(bpy.context.active_object)
-
-        container = base_layer.parent
-        filled_layer_name = f"{get_layer_name(base_layer)}_{self.from_min}-{self.from_max}-Filled"
-        scalar_offset = get_layer_meta(base_layer, "Scalar Offset")
-        base_shape = get_shape(base_layer)
-
-        base_grids = get_grids(base_layer)
-        base_volume = get_volume(base_grids, 0, base_shape)
-
-        mask = (base_volume > self.from_min + scalar_offset) \
-            & (base_volume < self.from_max + scalar_offset)
-        mask = scipy.median_filter(mask.astype(np.float32), size=2)
-
-        if self.invert:
-            base_volume = mask * base_volume + \
-                (1-mask) * (self.fill_value + scalar_offset)
-        else:
-            base_volume = (1-mask) * base_volume + \
-                mask * (self.fill_value + scalar_offset)
-
-        set_volume(base_grids, 0, base_volume)
-        vdb_path = save_vdb(base_grids, context)
-        filled_layer = deep_copy_layer(vdb_path,
-                                       base_layer,
-                                       f"{container.name}_{filled_layer_name}")
-        mask_node = add_mask_node(container,
-                                  filled_layer,
-                                  "BioxelNodes_MaskByThreshold",
-                                  filled_layer_name)
-
-        mask_node.inputs[1].default_value = self.from_min
-
-        select_object(container)
-
-        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        base_layer = get_layer(bpy.context.active_object)
-        scalar_min = get_layer_meta(base_layer, "Scalar Min")
-        self.fill_value = scalar_min
-        context.window_manager.invoke_props_dialog(self, width=400)
-        return {'RUNNING_MODAL'}
-
-
-class FillByLabel(bpy.types.Operator):
-    bl_idname = "bioxelnodes.fill_by_label"
-    bl_label = "Fill Value by Label"
-    bl_description = "Fill Value by Label Area"
-    bl_options = {'UNDO'}
-
-    label_layer: bpy.props.EnumProperty(
-        name="Label Layer",
-        items=get_label_layer_selection
-    )  # type: ignore
-
-    fill_value: bpy.props.FloatProperty(
-        name="Fill Value",
-        soft_min=0, soft_max=1024.0,
-        default=0,
-    )  # type: ignore
-
-    invert: bpy.props.BoolProperty(
-        name="Invert Label",
-        default=True,
-    )  # type: ignore
-
-    @classmethod
-    def poll(cls, context):
-        layer = get_layer(bpy.context.active_object)
-        if layer:
-            return layer.get("bioxel_layer_type") == "scalar"
-        else:
-            return False
-
-    def execute(self, context):
-        base_layer = get_layer(bpy.context.active_object)
-        label_layer = bpy.data.objects[self.label_layer]
-
-        if not label_layer:
-            self.report({"WARNING"}, "Cannot find any label layer.")
-            return {'FINISHED'}
-
-        container = base_layer.parent
-        filled_layer_name = f"{get_layer_name(base_layer)}_{get_layer_name(label_layer)}-Filled"
-        scalar_offset = get_layer_meta(base_layer, "Scalar Offset")
-        base_shape = get_shape(base_layer)
-        label_shape = get_shape(label_layer)
-
-        base_grids = get_grids(base_layer)
-        base_volume = get_volume(base_grids, 0, base_shape)
-
-        label_grids = get_grids(label_layer)
-        mask = get_volume(label_grids, 0, label_shape)
-        mask = ski.resize(mask,
-                          base_shape,
-                          preserve_range=True,
-                          anti_aliasing=True)
-        mask = scipy.median_filter(mask.astype(np.float32), size=2)
-
-        if self.invert:
-            base_volume = mask * base_volume + \
-                (1-mask) * (self.fill_value + scalar_offset)
-        else:
-            base_volume = (1-mask) * base_volume + \
-                mask * (self.fill_value + scalar_offset)
-
-        set_volume(base_grids, 0, base_volume)
-        vdb_path = save_vdb(base_grids, context)
-        filled_layer = deep_copy_layer(vdb_path,
-                                       base_layer,
-                                       f"{container.name}_{filled_layer_name}")
-        add_mask_node(container,
-                      filled_layer,
-                      "BioxelNodes_MaskByThreshold",
-                      filled_layer_name)
-
-        select_object(container)
-
-        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        base_layer = get_layer(bpy.context.active_object)
-        scalar_min = get_layer_meta(base_layer, "Scalar Min")
-        self.fill_value = scalar_min
-        context.window_manager.invoke_props_dialog(self, width=400)
-        return {'RUNNING_MODAL'}
-
-
-class CombineLabels(bpy.types.Operator):
-    bl_idname = "bioxelnodes.combine_labels"
-    bl_label = "Combine Labels"
-    bl_description = "Combine all selected labels"
-    bl_options = {'UNDO'}
-
-    @classmethod
-    def poll(cls, context):
-        labels = [obj for obj in context.selected_ids
-                  if obj.get("bioxel_layer_type") == "label"]
-        return True if len(labels) > 1 else False
-
-    def execute(self, context):
-        labels = [obj for obj in context.selected_ids
-                  if obj.get("bioxel_layer_type") == "label"]
-        base_layer = labels[0]
-        labels = labels[1:]
-        container = base_layer.parent
-        label_names = [get_layer_name(base_layer)]
-        base_shape = get_shape(base_layer)
-
-        base_grids = get_grids(base_layer)
-        base_volume = get_volume(base_grids, 0, base_shape)
-        base_volume = base_volume
-
-        for label in labels:
-            label_shape = get_shape(label)
-            label_grids = get_grids(label)
-            label_volume = get_volume(label_grids, 0, label_shape)
-            label_volume = ski.resize(label_volume,
-                                      base_shape,
-                                      preserve_range=True,
-                                      anti_aliasing=True)
-            base_volume = np.maximum(base_volume, label_volume)
-            label_names.append(get_layer_name(label))
-
-        set_volume(base_grids, 0, base_volume)
-
-        combined_layer_name = f"{'-'.join(label_names)}-Combined"
-        vdb_path = save_vdb(base_grids, context)
-        combined_layer = deep_copy_layer(vdb_path,
-                                         base_layer,
-                                         f"{container.name}_{combined_layer_name}")
-        add_mask_node(container,
-                      combined_layer,
-                      "BioxelNodes_MaskByLabel",
-                      combined_layer_name)
-
-        select_object(container)
-        return {'FINISHED'}
-
-
-class ConvertToMesh(bpy.types.Operator):
-    bl_idname = "bioxelnodes.convert_to_mesh"
-    bl_label = "Convert To Mesh"
-    bl_description = "Convert Container To Mesh"
-    bl_options = {'UNDO'}
-
-    @classmethod
-    def poll(cls, context):
-        containers = get_container_from_selection()
-        return len(containers) > 0
-
-    def execute(self, context):
-        containers = get_container_from_selection()
-
-        if len(containers) == 0:
-            self.report({"WARNING"}, "Cannot find any bioxel container.")
-            return {'FINISHED'}
-
-        container = containers[0]
-
-        bpy.ops.mesh.primitive_cube_add(
-            size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-        mesh = bpy.context.active_object
-
-        mesh.name = f"Mesh_{container.name}"
-
-        # bpy.ops.object.constraint_add(type='COPY_TRANSFORMS')
-        # mesh.constraints[0].target = container
-
-        bpy.ops.node.new_geometry_nodes_modifier()
-        modifier = mesh.modifiers[0]
-        node_group = modifier.node_group
-
-        output_node = get_nodes_by_type(node_group, 'NodeGroupOutput')[0]
-        to_mesh_node = custom_nodes.add_node(node_group,
-                                             "BioxelNodes_PickMesh")
-
-        to_mesh_node.inputs[0].default_value = container
-        node_group.links.new(to_mesh_node.outputs[0], output_node.inputs[0])
-
-        # bpy.ops.constraint.apply(
-        #     constraint=mesh.constraints[0].name, owner='OBJECT')
-        bpy.ops.object.modifier_apply(modifier=mesh.modifiers[0].name)
-
-        select_object(mesh)
-
-        self.report({"INFO"}, f"Successfully convert to mesh")
-
-        return {'FINISHED'}
-
-
-class PickMesh(bpy.types.Operator):
-    bl_idname = "bioxelnodes.pick_mesh"
-    bl_label = "Pick Mesh"
-    bl_description = "Pick Container Mesh"
-    bl_options = {'UNDO'}
-
-    @classmethod
-    def poll(cls, context):
-        containers = get_container_from_selection()
-        return len(containers) > 0
-
-    def execute(self, context):
-        containers = get_container_from_selection()
-
-        if len(containers) == 0:
-            self.report({"WARNING"}, "Cannot find any bioxel container.")
-            return {'FINISHED'}
-
-        container = containers[0]
-
-        bpy.ops.mesh.primitive_cube_add(
-            size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-        mesh = bpy.context.active_object
-
-        mesh.name = f"Mesh_{container.name}"
-
-        bpy.ops.node.new_geometry_nodes_modifier()
-        modifier = mesh.modifiers[0]
-        node_group = modifier.node_group
-
-        output_node = get_nodes_by_type(node_group, 'NodeGroupOutput')[0]
-        pick_mesh_node = custom_nodes.add_node(node_group,
-                                               "BioxelNodes_PickMesh")
-
-        pick_mesh_node.inputs[0].default_value = container
-        node_group.links.new(pick_mesh_node.outputs[0], output_node.inputs[0])
-
-        select_object(mesh)
-
-        self.report({"INFO"}, f"Successfully picked mesh")
-
-        return {'FINISHED'}
-
-
-class PickVolume(bpy.types.Operator):
-    bl_idname = "bioxelnodes.pick_volume"
-    bl_label = "Pick Volume"
-    bl_description = "Pick Container Volume"
-    bl_options = {'UNDO'}
-
-    @classmethod
-    def poll(cls, context):
-        containers = get_container_from_selection()
-        return len(containers) > 0
-
-    def execute(self, context):
-        containers = get_container_from_selection()
-
-        if len(containers) == 0:
-            self.report({"WARNING"}, "Cannot find any bioxel container.")
-            return {'FINISHED'}
-
-        container = containers[0]
-
-        bpy.ops.mesh.primitive_cube_add(
-            size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-        volume = bpy.context.active_object
-
-        volume.name = f"Volume_{container.name}"
-
-        bpy.ops.node.new_geometry_nodes_modifier()
-        modifier = volume.modifiers[0]
-        node_group = modifier.node_group
-
-        output_node = get_nodes_by_type(node_group, 'NodeGroupOutput')[0]
-        pick_volume_node = custom_nodes.add_node(node_group,
-                                                 "BioxelNodes_PickVolume")
-
-        pick_volume_node.inputs[0].default_value = container
-        node_group.links.new(
-            pick_volume_node.outputs[0], output_node.inputs[0])
-
-        select_object(volume)
-
-        self.report({"INFO"}, f"Successfully picked volume")
-
-        return {'FINISHED'}
-
-
-class PickBboxWire(bpy.types.Operator):
-    bl_idname = "bioxelnodes.pick_bbox_wire"
-    bl_label = "Pick Bbox Wire"
-    bl_description = "Pick Container Bbox Wire"
-    bl_options = {'UNDO'}
-
-    @classmethod
-    def poll(cls, context):
-        containers = get_container_from_selection()
-        return len(containers) > 0
-
-    def execute(self, context):
-        containers = get_container_from_selection()
-
-        if len(containers) == 0:
-            self.report({"WARNING"}, "Cannot find any bioxel container.")
-            return {'FINISHED'}
-
-        container = containers[0]
-
-        bpy.ops.mesh.primitive_cube_add(
-            size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-        bbox_wire = bpy.context.active_object
-
-        bbox_wire.name = f"Wire_{container.name}"
-
-        bpy.ops.node.new_geometry_nodes_modifier()
-        modifier = bbox_wire.modifiers[0]
-        node_group = modifier.node_group
-
-        output_node = get_nodes_by_type(node_group, 'NodeGroupOutput')[0]
-        pick_bbox_wire_node = custom_nodes.add_node(node_group,
-                                                    "BioxelNodes_PickBboxWire")
-
-        pick_bbox_wire_node.inputs[0].default_value = container
-        node_group.links.new(
-            pick_bbox_wire_node.outputs[0], output_node.inputs[0])
-
-        select_object(bbox_wire)
-
-        self.report({"INFO"}, f"Successfully picked bbox wire")
-
-        return {'FINISHED'}
-
-
-class AddCutter():
-    bl_options = {'UNDO'}
-
-    @classmethod
-    def poll(cls, context):
-        containers = get_container_from_selection()
-        return len(containers) > 0
-
-    def execute(self, context):
-        containers = get_container_from_selection()
-
-        if len(containers) == 0:
-            self.report({"WARNING"}, "Cannot find any bioxel container.")
-            return {'FINISHED'}
-
-        container = containers[0]
-
-        if self.object_type == "plane":
-            node_type = "BioxelNodes_PlaneObjectCutter"
-            bpy.ops.mesh.primitive_plane_add(
-                size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-        elif self.object_type == "cylinder":
-            node_type = "BioxelNodes_CylinderObjectCutter"
-            bpy.ops.mesh.primitive_cylinder_add(
-                radius=1, depth=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-            bpy.context.object.rotation_euler[0] = container.rotation_euler[0]
-        elif self.object_type == "cube":
-            node_type = "BioxelNodes_CubeObjectCutter"
-            bpy.ops.mesh.primitive_cube_add(
-                size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-        elif self.object_type == "sphere":
-            node_type = "BioxelNodes_SphereObjectCutter"
-            bpy.ops.mesh.primitive_ico_sphere_add(
-                radius=1, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-        elif self.object_type == "pie":
-            node_type = "BioxelNodes_PieObjectCutter"
-            # Create mesh
-            pie_mesh = bpy.data.meshes.new('Pie')
-
-            # Create object
-            pie = bpy.data.objects.new('Pie', pie_mesh)
-
-            # Link object to scene
-            bpy.context.scene.collection.objects.link(pie)
-            # Get a BMesh representation
-            bm = bmesh.new()   # create an empty BMesh
-            bm.from_mesh(pie_mesh)   # fill it in from a Mesh
-
-            # Hot to create vertices
-            v_0 = bm.verts.new((0.0, -1.0, 0.0))
-            v_1 = bm.verts.new((-1.0, -1.0, 1.0))
-            v_2 = bm.verts.new((0.0, 1.0, 0.0))
-            v_3 = bm.verts.new((-1.0, 1.0, 1.0))
-            v_4 = bm.verts.new((1.0, -1.0, 1.0))
-            v_5 = bm.verts.new((1.0, 1.0, 1.0))
-
-            # Initialize the index values of this sequence.
-            bm.verts.index_update()
-
-            # How to create a face
-            # it's not necessary to create the edges before, I made it only to show how create
-            # edges too
-            bm.faces.new((v_0, v_1, v_3, v_2))
-            bm.faces.new((v_0, v_2, v_5, v_4))
-
-            # Finish up, write the bmesh back to the mesh
-            bm.to_mesh(pie_mesh)
-            bpy.context.view_layer.objects.active = pie
-
-        cutter = bpy.context.active_object
-        cutter.visible_camera = False
-        cutter.visible_diffuse = False
-        cutter.visible_glossy = False
-        cutter.visible_transmission = False
-        cutter.visible_volume_scatter = False
-        cutter.visible_shadow = False
-        cutter.hide_render = True
-        cutter.display_type = 'WIRE'
-
-        modifier = container.modifiers[0]
-        node_group = modifier.node_group
-        cutter_node = custom_nodes.add_node(node_group, node_type)
-        cutter_node.inputs[0].default_value = cutter
-
-        cut_nodes = get_nodes_by_type(node_group,
-                                      'BioxelNodes_Cut')
-        output_node = get_nodes_by_type(node_group, 'NodeGroupOutput')[0]
-        if len(cut_nodes) == 0:
-            cut_node = custom_nodes.add_node(node_group, 'BioxelNodes_Cut')
-            if len(output_node.inputs[0].links) == 0:
-                node_group.links.new(cut_node.outputs[0],
-                                     output_node.inputs[0])
-                move_node_to_node(cut_node, output_node, (-300, 0))
-            else:
-                pre_output_node = output_node.inputs[0].links[0].from_node
-                node_group.links.new(pre_output_node.outputs[0],
-                                     cut_node.inputs[0])
-                node_group.links.new(cut_node.outputs[0],
-                                     output_node.inputs[0])
-                move_node_between_nodes(cut_node,
-                                        [pre_output_node, output_node])
-
-            node_group.links.new(cutter_node.outputs[0],
-                                 cut_node.inputs[1])
-
-            move_node_to_node(cutter_node, cut_node, (-300, -300))
-            select_object(cutter)
-        else:
-            move_node_to_node(cutter_node, output_node, (0, -100))
-            select_object(container)
-
-        return {'FINISHED'}
-
-
-class AddPlaneCutter(bpy.types.Operator, AddCutter):
-    bl_idname = "bioxelnodes.add_plane_cutter"
-    bl_label = "Add a Plane Cutter"
-    bl_description = "Add a Plane Cutter to Container"
-    bl_options = {'UNDO'}
-    object_type = "plane"
-
-
-class AddCylinderCutter(bpy.types.Operator, AddCutter):
-    bl_idname = "bioxelnodes.add_cylinder_cutter"
-    bl_label = "Add a Cylinder Cutter"
-    bl_description = "Add a Cylinder Cutter to Container"
-    bl_options = {'UNDO'}
-    object_type = "cylinder"
-
-
-class AddCubeCutter(bpy.types.Operator, AddCutter):
-    bl_idname = "bioxelnodes.add_cube_cutter"
-    bl_label = "Add a Cube Cutter"
-    bl_description = "Add a Cube Cutter to Container"
-    bl_options = {'UNDO'}
-    object_type = "cube"
-
-
-class AddSphereCutter(bpy.types.Operator, AddCutter):
-    bl_idname = "bioxelnodes.add_sphere_cutter"
-    bl_label = "Add a Sphere Cutter"
-    bl_description = "Add a Sphere Cutter to Container"
-    bl_options = {'UNDO'}
-    object_type = "sphere"
-
-
-class AddPieCutter(bpy.types.Operator, AddCutter):
-    bl_idname = "bioxelnodes.add_pie_cutter"
-    bl_label = "Add a Pie Cutter"
-    bl_description = "Add a Pie Cutter to Container"
-    bl_options = {'UNDO'}
-    object_type = "pie"

bioxelnodes/operators/container.py

@@ -0,0 +1,290 @@
+import bpy
+
+
+import bmesh
+
+from ..nodes import custom_nodes
+from ..bioxel.io import load_container, save_container
+from ..bioxelutils.layer import get_all_layer_objs
+from ..bioxelutils.container import (container_to_obj, obj_to_container,
+                                     get_container_objs_from_selection)
+from ..bioxelutils.node import get_nodes_by_type, move_node_between_nodes, move_node_to_node
+from .utils import change_render_setting, get_cache_dir, get_preferences, select_object
+
+
+class SaveContainer(bpy.types.Operator):
+    bl_idname = "bioxelnodes.save_container"
+    bl_label = "Save Container (.bioxel) (BETA)"
+    bl_description = "Clean all caches saved in temp"
+
+    filepath: bpy.props.StringProperty(
+        subtype="FILE_PATH"
+    )  # type: ignore
+
+    filename_ext = ".bioxel"
+
+    @classmethod
+    def poll(cls, context):
+        container_objs = get_container_objs_from_selection()
+        return len(container_objs) > 0
+
+    def execute(self, context):
+        container_objs = get_container_objs_from_selection()
+
+        if len(container_objs) == 0:
+            self.report({"WARNING"}, "Cannot find any bioxel container.")
+            return {'FINISHED'}
+
+        container = obj_to_container(container_objs[0])
+        save_path = f"{self.filepath.split('.')[0]}.bioxel"
+        save_container(container, save_path, overwrite=True)
+
+        self.report({"INFO"}, f"Successfully save to {save_path}")
+        return {'FINISHED'}
+
+    def invoke(self, context, event):
+        context.window_manager.fileselect_add(self)
+        return {'RUNNING_MODAL'}
+
+
+class LoadContainer(bpy.types.Operator):
+    bl_idname = "bioxelnodes.load_container"
+    bl_label = "Load Container (.bioxel) (BETA)"
+    bl_description = "Clean all caches saved in temp"
+
+    filepath: bpy.props.StringProperty(
+        subtype="FILE_PATH"
+    )  # type: ignore
+
+    filename_ext = ".bioxel"
+
+    def execute(self, context):
+        load_path = self.filepath
+        container = load_container(self.filepath)
+        is_first_import = len(get_all_layer_objs()) == 0
+
+        container_obj = container_to_obj(container,
+                                         scene_scale=0.01,
+                                         cache_dir=get_cache_dir(context))
+        select_object(container_obj)
+
+        if is_first_import:
+            change_render_setting(context)
+
+        self.report({"INFO"}, f"Successfully load {load_path}")
+        return {'FINISHED'}
+
+    def invoke(self, context, event):
+        context.window_manager.fileselect_add(self)
+        return {'RUNNING_MODAL'}
+
+
+class PickObject():
+    bl_options = {'UNDO'}
+
+    @classmethod
+    def poll(cls, context):
+        container_objs = get_container_objs_from_selection()
+        return len(container_objs) > 0
+
+    def execute(self, context):
+        container_objs = get_container_objs_from_selection()
+
+        if len(container_objs) == 0:
+            self.report({"WARNING"}, "Cannot find any bioxel container.")
+            return {'FINISHED'}
+
+        container_obj = container_objs[0]
+
+        bpy.ops.mesh.primitive_cube_add(
+            size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
+        obj = bpy.context.active_object
+
+        obj.name = f"{self.object_type}_{container_obj.name}"
+
+        bpy.ops.node.new_geometry_nodes_modifier()
+        modifier = obj.modifiers[0]
+        node_group = modifier.node_group
+
+        output_node = get_nodes_by_type(node_group, 'NodeGroupOutput')[0]
+        pick_mesh_node = custom_nodes.add_node(node_group,
+                                               f"BioxelNodes_Pick{self.object_type}")
+
+        pick_mesh_node.inputs[0].default_value = container_obj
+        node_group.links.new(pick_mesh_node.outputs[0], output_node.inputs[0])
+
+        select_object(obj)
+
+        self.report({"INFO"}, f"Successfully picked")
+
+        return {'FINISHED'}
+
+
+class PickMesh(bpy.types.Operator, PickObject):
+    bl_idname = "bioxelnodes.pick_mesh"
+    bl_label = "Pick Mesh"
+    bl_description = "Pick Container Mesh"
+    object_type = "Mesh"
+
+
+class PickVolume(bpy.types.Operator, PickObject):
+    bl_idname = "bioxelnodes.pick_volume"
+    bl_label = "Pick Volume"
+    bl_description = "Pick Container Volume"
+    object_type = "Volume"
+
+
+class PickBboxWire(bpy.types.Operator, PickObject):
+    bl_idname = "bioxelnodes.pick_bbox_wire"
+    bl_label = "Pick Bbox Wire"
+    bl_description = "Pick Container Bbox Wire"
+    object_type = "BboxWire"
+
+
+class AddCutter():
+    bl_options = {'UNDO'}
+
+    @classmethod
+    def poll(cls, context):
+        container_objs = get_container_objs_from_selection()
+        return len(container_objs) > 0
+
+    def execute(self, context):
+        container_objs = get_container_objs_from_selection()
+
+        if len(container_objs) == 0:
+            self.report({"WARNING"}, "Cannot find any bioxel container.")
+            return {'FINISHED'}
+
+        container_obj = container_objs[0]
+
+        if self.object_type == "plane":
+            node_type = "BioxelNodes_PlaneObjectCutter"
+            bpy.ops.mesh.primitive_plane_add(
+                size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
+        elif self.object_type == "cylinder":
+            node_type = "BioxelNodes_CylinderObjectCutter"
+            bpy.ops.mesh.primitive_cylinder_add(
+                radius=1, depth=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
+            bpy.context.object.rotation_euler[0] = container_obj.rotation_euler[0]
+        elif self.object_type == "cube":
+            node_type = "BioxelNodes_CubeObjectCutter"
+            bpy.ops.mesh.primitive_cube_add(
+                size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
+        elif self.object_type == "sphere":
+            node_type = "BioxelNodes_SphereObjectCutter"
+            bpy.ops.mesh.primitive_ico_sphere_add(
+                radius=1, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
+        elif self.object_type == "pie":
+            node_type = "BioxelNodes_PieObjectCutter"
+            # Create mesh
+            pie_mesh = bpy.data.meshes.new('Pie')
+
+            # Create object
+            pie = bpy.data.objects.new('Pie', pie_mesh)
+
+            # Link object to scene
+            bpy.context.scene.collection.objects.link(pie)
+            # Get a BMesh representation
+            bm = bmesh.new()   # create an empty BMesh
+            bm.from_mesh(pie_mesh)   # fill it in from a Mesh
+
+            # Hot to create vertices
+            v_0 = bm.verts.new((0.0, -1.0, 0.0))
+            v_1 = bm.verts.new((-1.0, -1.0, 1.0))
+            v_2 = bm.verts.new((0.0, 1.0, 0.0))
+            v_3 = bm.verts.new((-1.0, 1.0, 1.0))
+            v_4 = bm.verts.new((1.0, -1.0, 1.0))
+            v_5 = bm.verts.new((1.0, 1.0, 1.0))
+
+            # Initialize the index values of this sequence.
+            bm.verts.index_update()
+
+            # How to create a face
+            # it's not necessary to create the edges before, I made it only to show how create
+            # edges too
+            bm.faces.new((v_0, v_1, v_3, v_2))
+            bm.faces.new((v_0, v_2, v_5, v_4))
+
+            # Finish up, write the bmesh back to the mesh
+            bm.to_mesh(pie_mesh)
+            bpy.context.view_layer.objects.active = pie
+
+        cutter_obj = bpy.context.active_object
+        cutter_obj.visible_camera = False
+        cutter_obj.visible_diffuse = False
+        cutter_obj.visible_glossy = False
+        cutter_obj.visible_transmission = False
+        cutter_obj.visible_volume_scatter = False
+        cutter_obj.visible_shadow = False
+        cutter_obj.hide_render = True
+        cutter_obj.display_type = 'WIRE'
+
+        modifier = container_obj.modifiers[0]
+        node_group = modifier.node_group
+        cutter_node = custom_nodes.add_node(node_group, node_type)
+        cutter_node.inputs[0].default_value = cutter_obj
+
+        cut_nodes = get_nodes_by_type(node_group,
+                                      'BioxelNodes_Cut')
+        output_node = get_nodes_by_type(node_group, 'NodeGroupOutput')[0]
+        if len(cut_nodes) == 0:
+            cut_node = custom_nodes.add_node(node_group, 'BioxelNodes_Cut')
+            if len(output_node.inputs[0].links) == 0:
+                node_group.links.new(cut_node.outputs[0],
+                                     output_node.inputs[0])
+                move_node_to_node(cut_node, output_node, (-300, 0))
+            else:
+                pre_output_node = output_node.inputs[0].links[0].from_node
+                node_group.links.new(pre_output_node.outputs[0],
+                                     cut_node.inputs[0])
+                node_group.links.new(cut_node.outputs[0],
+                                     output_node.inputs[0])
+                move_node_between_nodes(cut_node,
+                                        [pre_output_node, output_node])
+
+            node_group.links.new(cutter_node.outputs[0],
+                                 cut_node.inputs[1])
+
+            move_node_to_node(cutter_node, cut_node, (-300, -300))
+            select_object(cutter_obj)
+        else:
+            move_node_to_node(cutter_node, output_node, (0, -100))
+            select_object(container_obj)
+
+        return {'FINISHED'}
+
+
+class AddPlaneCutter(bpy.types.Operator, AddCutter):
+    bl_idname = "bioxelnodes.add_plane_cutter"
+    bl_label = "Add a Plane Cutter"
+    bl_description = "Add a Plane Cutter to Container"
+    object_type = "plane"
+
+
+class AddCylinderCutter(bpy.types.Operator, AddCutter):
+    bl_idname = "bioxelnodes.add_cylinder_cutter"
+    bl_label = "Add a Cylinder Cutter"
+    bl_description = "Add a Cylinder Cutter to Container"
+    object_type = "cylinder"
+
+
+class AddCubeCutter(bpy.types.Operator, AddCutter):
+    bl_idname = "bioxelnodes.add_cube_cutter"
+    bl_label = "Add a Cube Cutter"
+    bl_description = "Add a Cube Cutter to Container"
+    object_type = "cube"
+
+
+class AddSphereCutter(bpy.types.Operator, AddCutter):
+    bl_idname = "bioxelnodes.add_sphere_cutter"
+    bl_label = "Add a Sphere Cutter"
+    bl_description = "Add a Sphere Cutter to Container"
+    object_type = "sphere"
+
+
+class AddPieCutter(bpy.types.Operator, AddCutter):
+    bl_idname = "bioxelnodes.add_pie_cutter"
+    bl_label = "Add a Pie Cutter"
+    bl_description = "Add a Pie Cutter to Container"
+    object_type = "pie"

bioxelnodes/operators/io.py

@@ -0,0 +1,795 @@
+import math
+import bpy
+import shutil
+import threading
+import numpy as np
+from pathlib import Path
+
+
+from ..exceptions import CancelledByUser
+from ..props import BIOXELNODES_Series
+from ..bioxel.layer import Layer
+from ..bioxelutils.layer import (get_all_layer_objs,
+                                 get_layer_obj)
+from ..bioxelutils.container import (Container,
+                                     add_layers,
+                                     container_to_obj,
+                                     get_container_objs_from_selection)
+from ..bioxel.parse import (DICOM_EXTS, SUPPORT_EXTS,
+                            get_ext, parse_volumetric_data)
+from .utils import (change_render_setting, get_cache_dir, get_preferences,
+                    progress_update, progress_bar, select_object)
+
+# 3rd-party
+import SimpleITK as sitk
+import transforms3d
+
+
+def get_layer_shape(bioxel_size: float, orig_shape: tuple, orig_spacing: tuple):
+    shape = (int(orig_shape[0] / bioxel_size * orig_spacing[0]),
+             int(orig_shape[1] / bioxel_size * orig_spacing[1]),
+             int(orig_shape[2] / bioxel_size * orig_spacing[2]))
+
+    return (shape[0] if shape[0] > 0 else 1,
+            shape[1] if shape[1] > 0 else 1,
+            shape[2] if shape[2] > 0 else 1)
+
+
+def get_layer_size(shape: tuple, bioxel_size: float, scale: float = 1.0):
+    size = (float(shape[0] * bioxel_size * scale),
+            float(shape[1] * bioxel_size * scale),
+            float(shape[2] * bioxel_size * scale))
+
+    return size
+
+
+"""
+ImportVolumetricData
+                        -> ParseVolumetricData -> ImportVolumetricDataDialog
+FH_ImportVolumetricData
+
+ start import                  parse data               execute import
+"""
+
+
+class ImportVolumetricData():
+    bl_options = {'UNDO'}
+
+    filepath: bpy.props.StringProperty(subtype="FILE_PATH")  # type: ignore
+
+    read_as = "scalar"
+
+    def execute(self, context):
+        data_path = Path(self.filepath).resolve()
+        ext = get_ext(data_path)
+        if ext not in SUPPORT_EXTS:
+            self.report({"WARNING"}, "Not supported format.")
+            return {'CANCELLED'}
+
+        bpy.ops.bioxelnodes.parse_volumetric_data('INVOKE_DEFAULT',
+                                                  filepath=self.filepath,
+                                                  skip_read_as=True,
+                                                  read_as=self.read_as)
+
+        return {'FINISHED'}
+
+    def invoke(self, context, event):
+        context.window_manager.fileselect_add(self)
+        return {'RUNNING_MODAL'}
+
+
+class ImportAsScalarLayer(bpy.types.Operator, ImportVolumetricData):
+    bl_idname = "bioxelnodes.import_as_scalar_layer"
+    bl_label = "Import as Scalar"
+    bl_description = "Import Volumetric Data to Container as Scalar"
+    read_as = "scalar"
+
+
+class ImportAsLabelLayer(bpy.types.Operator, ImportVolumetricData):
+    bl_idname = "bioxelnodes.import_as_label_layer"
+    bl_label = "Import as Label"
+    bl_description = "Import Volumetric Data to Container as Label"
+    read_as = "label"
+
+
+class BIOXELNODES_FH_ImportVolumetricData(bpy.types.FileHandler):
+    bl_idname = "BIOXELNODES_FH_ImportVolumetricData"
+    bl_label = "File handler for dicom import"
+    bl_import_operator = "bioxelnodes.parse_volumetric_data"
+    bl_file_extensions = ";".join(SUPPORT_EXTS)
+
+    @classmethod
+    def poll_drop(cls, context):
+        return (context.area and context.area.type == 'VIEW_3D')
+
+
+def get_series_ids(self, context):
+    items = []
+    for index, series_id in enumerate(self.series_ids):
+        items.append((
+            series_id.id,
+            series_id.label,
+            "",
+            index
+        ))
+
+    return items
+
+
+class ParseVolumetricData(bpy.types.Operator):
+    bl_idname = "bioxelnodes.parse_volumetric_data"
+    bl_label = "Import Volumetric Data (BioxelNodes)"
+    bl_description = "Import Volumetric Data as Layer"
+    bl_options = {'UNDO'}
+
+    meta = None
+    thread = None
+    _timer = None
+    container_obj_name = ""
+
+    progress: bpy.props.FloatProperty(name="Progress",
+                                      options={"SKIP_SAVE"},
+                                      default=1)  # type: ignore
+
+    filepath: bpy.props.StringProperty(subtype="FILE_PATH")  # type: ignore
+
+    skip_read_as: bpy.props.BoolProperty(name="Skip Read As",
+                                         default=False,
+                                         options={"SKIP_SAVE"})  # type: ignore
+
+    skip_series_select: bpy.props.BoolProperty(name="Skip Sries Select",
+                                               default=True,
+                                               options={"SKIP_SAVE"})  # type: ignore
+
+    read_as: bpy.props.EnumProperty(name="Read as",
+                                    default="scalar",
+                                    items=[("scalar", "Scalar", ""),
+                                           ("label", "Labels", "")])  # type: ignore
+
+    series_id: bpy.props.EnumProperty(name="Select Series",
+                                      items=get_series_ids)  # type: ignore
+
+    series_ids: bpy.props.CollectionProperty(
+        type=BIOXELNODES_Series)  # type: ignore
+
+    def execute(self, context):
+        data_path = Path(self.filepath).resolve()
+        ext = get_ext(data_path)
+        if ext not in SUPPORT_EXTS:
+            self.report({"WARNING"}, "Not supported format.")
+            return {'CANCELLED'}
+
+        print("Collecting Meta Data...")
+
+        def parse_volumetric_data_func(self, context, cancel):
+            def progress_callback(factor, text):
+                if cancel():
+                    raise CancelledByUser
+                progress_update(context, factor, text)
+
+            try:
+                series_id = self.series_id if self.series_id != "empty" else ""
+                data, meta = parse_volumetric_data(data_file=self.filepath,
+                                                   series_id=series_id,
+                                                   progress_callback=progress_callback)
+            except CancelledByUser:
+                return
+            except Exception as e:
+                self.has_error = e
+                return
+
+            if cancel():
+                return
+
+            self.meta = meta
+
+        # Init cancel flag
+        self.is_cancelled = False
+        self.has_error = None
+
+        # Create the thread
+        self.thread = threading.Thread(target=parse_volumetric_data_func,
+                                       args=(self, context, lambda: self.is_cancelled))
+
+        # Start the thread
+        self.thread.start()
+        # Add a timmer for modal
+        self._timer = context.window_manager.event_timer_add(time_step=0.1,
+                                                             window=context.window)
+        # Append progress bar to status bar
+        bpy.types.STATUSBAR_HT_header.append(progress_bar)
+
+        # Start modal handler
+        context.window_manager.modal_handler_add(self)
+        return {'RUNNING_MODAL'}
+
+    def modal(self, context, event):
+        # Check if user press 'ESC'
+        if event.type == 'ESC':
+            self.is_cancelled = True
+            progress_update(context, 0, "Canceling...")
+            return {'PASS_THROUGH'}
+
+        # Check if is the timer time
+        if event.type != 'TIMER':
+            return {'PASS_THROUGH'}
+
+        # Force update status bar
+        bpy.context.workspace.status_text_set_internal(None)
+
+        # Check if thread is still running
+        if self.thread.is_alive():
+            return {'PASS_THROUGH'}
+
+        # Release the thread
+        self.thread.join()
+        # Remove the timer
+        context.window_manager.event_timer_remove(self._timer)
+        # Remove the progress bar from status bar
+        bpy.types.STATUSBAR_HT_header.remove(progress_bar)
+
+        # Check if thread is cancelled by user
+        if self.is_cancelled:
+            self.report({"WARNING"}, "Canncelled by user.")
+            return {'CANCELLED'}
+
+        # Check if thread is cancelled by user
+        if self.has_error:
+            raise self.has_error
+
+        # Check if has return
+        if self.meta is None:
+            self.report({"ERROR"}, "Some thing went wrong.")
+            return {'CANCELLED'}
+
+        # If not canncelled...
+        for key, value in self.meta.items():
+            print(f"{key}: {value}")
+
+        orig_shape = self.meta['xyz_shape']
+        orig_spacing = self.meta['spacing']
+        min_size = min(orig_spacing[0],
+                       orig_spacing[1], orig_spacing[2])
+        bioxel_size = max(min_size, 1.0)
+
+        layer_shape = get_layer_shape(1, orig_shape, orig_spacing)
+        layer_size = get_layer_size(layer_shape,
+                                    bioxel_size)
+        log10 = math.floor(math.log10(max(*layer_size)))
+        log10 = max(1, log10)
+        log10 = min(3, log10)
+        scene_scale = math.pow(10, -log10)
+
+        if self.container_obj_name:
+            container_obj = bpy.data.objects.get(self.container_obj_name)
+            container_name = container_obj.name
+        else:
+            container_name = self.meta['name']
+
+        series_id = self.series_id if self.series_id != "empty" else ""
+        bpy.ops.bioxelnodes.import_volumetric_data_dialog(
+            'INVOKE_DEFAULT',
+            filepath=self.filepath,
+            container_name=container_name,
+            layer_name=self.meta['description'],
+            orig_shape=orig_shape,
+            orig_spacing=orig_spacing,
+            bioxel_size=bioxel_size,
+            series_id=series_id,
+            frame_count=self.meta['frame_count'],
+            channel_count=self.meta['channel_count'],
+            container_obj_name=self.container_obj_name,
+            read_as=self.read_as,
+            scene_scale=scene_scale
+        )
+
+        self.report({"INFO"}, "Successfully Readed.")
+        return {'FINISHED'}
+
+    def invoke(self, context, event):
+        if not self.filepath:
+            return {'CANCELLED'}
+
+        data_path = Path(self.filepath).resolve()
+        ext = get_ext(data_path)
+
+        container_objs = get_container_objs_from_selection()
+        if len(container_objs) > 0:
+            self.container_obj_name = container_objs[0].name
+
+        title = f"Add to **{self.container_obj_name}**" \
+            if self.container_obj_name != "" else f"Init a Container"
+
+        # Series Selection
+        if ext in DICOM_EXTS:
+            data_dirpath = data_path.parent
+            reader = sitk.ImageSeriesReader()
+            reader.MetaDataDictionaryArrayUpdateOn()
+            reader.LoadPrivateTagsOn()
+
+            series_ids = reader.GetGDCMSeriesIDs(str(data_dirpath))
+            series_items = {}
+
+            for series_id in series_ids:
+                series_files = reader.GetGDCMSeriesFileNames(
+                    str(data_dirpath), series_id)
+                single = sitk.ImageFileReader()
+                single.SetFileName(series_files[0])
+                single.LoadPrivateTagsOn()
+                single.ReadImageInformation()
+
+                def get_meta(key):
+                    try:
+                        stirng = single.GetMetaData(key).removesuffix(" ")
+                        if stirng in ["No study description",
+                                      "No series description",
+                                      ""]:
+                            return "Unknown"
+                        else:
+                            return stirng
+                    except:
+                        return "Unknown"
+
+                study_description = get_meta("0008|1030")
+                series_description = get_meta("0008|103e")
+                series_modality = get_meta("0008|0060")
+                size_x = get_meta("0028|0011")
+                size_y = get_meta("0028|0010")
+                count = get_meta("0020|0013")
+                count = count if count != "Unknown" else 1
+
+                # some series image count = 0 ????
+                if int(count) == 0:
+                    continue
+
+                # series_id cannot be "" in blender selection
+                if series_id == "":
+                    series_id = "empty"
+
+                series_items[series_id] = "{:<20} {:>1}".format(f"{study_description}>{series_description}({series_modality})",
+                                                                f"({size_x}x{size_y})x{count}")
+
+            for key, value in series_items.items():
+                series_item = self.series_ids.add()
+                series_item.id = key
+                series_item.label = value
+
+            if len(series_items.keys()) > 1:
+                self.skip_series_select = False
+                context.window_manager.invoke_props_dialog(self,
+                                                           width=400,
+                                                           title=title)
+                return {'RUNNING_MODAL'}
+            elif len(series_items.keys()) == 1:
+                self.series_id = list(series_items.keys())[0]
+            else:
+                self.report({"ERROR"}, "Get no vaild series.")
+                return {'CANCELLED'}
+
+        if self.skip_read_as:
+            self.execute(context)
+            return {'RUNNING_MODAL'}
+        else:
+            context.window_manager.invoke_props_dialog(self,
+                                                       width=400,
+                                                       title=title)
+            return {'RUNNING_MODAL'}
+
+    def draw(self, context):
+        layout = self.layout
+        if not self.skip_read_as:
+            layout.label(
+                text='What kind is the data read as?')
+            layout.prop(self, "read_as")
+        if not self.skip_series_select:
+            layout.label(text='Which series to import?')
+            layout.prop(self, "series_id")
+
+
+def get_sequence_sources(self, context):
+    items = [("-1", "None (1 frame)", "")]
+    orig_shape = tuple(self.orig_shape)
+    if self.frame_count > 1:
+        items.append(("0", f"Frame ({self.frame_count} frames)", ""))
+    elif self.frame_count == 1 and self.channel_count > 1:
+        items.append(("4", f"Channel ({self.channel_count} frames)", ""))
+    elif self.frame_count == 1 and self.channel_count == 1:
+        items.append(("1", f"X ({orig_shape[0]} frames)", ""))
+        items.append(("2", f"Y ({orig_shape[1]} frames)", ""))
+        items.append(("3", f"Z ({orig_shape[2]} frames)", ""))
+
+    return items
+
+
+class ImportVolumetricDataDialog(bpy.types.Operator):
+    bl_idname = "bioxelnodes.import_volumetric_data_dialog"
+    bl_label = "Import Volumetric Data"
+    bl_description = "Import Volumetric Data as Layer"
+    bl_options = {'UNDO'}
+
+    layers = None
+    thread = None
+    _timer = None
+
+    filepath: bpy.props.StringProperty(subtype="FILE_PATH")  # type: ignore
+
+    container_name: bpy.props.StringProperty(
+        name="Container Name")   # type: ignore
+
+    layer_name: bpy.props.StringProperty(name="Layer Name")   # type: ignore
+
+    series_id: bpy.props.StringProperty()   # type: ignore
+
+    container_obj_name: bpy.props.StringProperty()   # type: ignore
+
+    frame_count: bpy.props.IntProperty()  # type: ignore
+
+    channel_count: bpy.props.IntProperty()  # type: ignore
+
+    read_as: bpy.props.EnumProperty(name="Read as",
+                                    default="scalar",
+                                    items=[("scalar", "Scalar", ""),
+                                           ("label", "Labels", "")])  # type: ignore
+
+    bioxel_size: bpy.props.FloatProperty(name="Bioxel Size (Larger size means small resolution)",
+                                         soft_min=0.1, soft_max=10.0,
+                                         min=0.1, max=1e2,
+                                         default=1)  # type: ignore
+
+    orig_spacing: bpy.props.FloatVectorProperty(name="Original Spacing",
+                                                default=(1, 1, 1))  # type: ignore
+
+    orig_shape: bpy.props.IntVectorProperty(name="Original Shape",
+                                            default=(100, 100, 100))  # type: ignore
+
+    scene_scale: bpy.props.FloatProperty(name="Scene Scale (Bioxel Unit pre Blender Unit)",
+                                         soft_min=0.0001, soft_max=10.0,
+                                         min=1e-6, max=1e6,
+                                         default=0.01)  # type: ignore
+
+    split_channels: bpy.props.BoolProperty(name="Split Channels",
+                                           default=False)  # type: ignore
+
+    sequence_source: bpy.props.EnumProperty(name="Time Sequence From",
+                                            items=get_sequence_sources)  # type: ignore
+
+    def execute(self, context):
+        def import_volumetric_data_func(self, context, cancel):
+            progress_update(context, 0.0, "Parsing Volumetirc Data...")
+
+            def progress_callback(factor, text):
+                if cancel():
+                    raise CancelledByUser
+                progress_update(context, factor*0.2, text)
+
+            try:
+                data, meta = parse_volumetric_data(data_file=self.filepath,
+                                                   series_id=self.series_id,
+                                                   progress_callback=progress_callback)
+            except CancelledByUser:
+                return
+            except Exception as e:
+                self.has_error = e
+                return
+
+            if cancel():
+                return
+
+            shape = get_layer_shape(self.bioxel_size,
+                                    self.orig_shape,
+                                    self.orig_spacing)
+
+            mat_scale = transforms3d.zooms.zfdir2aff(self.bioxel_size)
+            affine = np.dot(meta['affine'], mat_scale)
+            kind = self.read_as
+
+            if cancel():
+                return
+
+            # change shape as sequence or not
+            if self.sequence_source == "-1":
+                data = data[0:1, :, :, :, :]
+            elif self.sequence_source == "0":
+                # frame as frame
+                pass
+            elif self.sequence_source == "1":
+                # X as frame
+                data = data.transpose(1, 0, 2, 3, 4)
+                shape = (1, shape[1], shape[2])
+            elif self.sequence_source == "2":
+                # Y as frame
+                data = data.transpose(2, 1, 0, 3, 4)
+                shape = (shape[0], 1, shape[2])
+            elif self.sequence_source == "3":
+                # Z as frame
+                data = data.transpose(3, 1, 2, 0, 4)
+                shape = (shape[0], shape[1], 1)
+            else:
+                # channel as frame
+                data = data.transpose(4, 1, 2, 3, 0)
+
+            def progress_callback_factory(layer_name, progress, progress_step):
+                def progress_callback(frame, total):
+                    if cancel():
+                        raise CancelledByUser
+                    sub_progress_step = progress_step/total
+                    sub_progress = progress + frame * sub_progress_step
+                    progress_update(context, sub_progress,
+                                    f"Processing {layer_name} Frame {frame+1}...")
+                return progress_callback
+
+            layers = []
+            if kind == "label":
+                name = self.layer_name or "Label"
+                data = data.astype(int)
+                label_count = int(np.max(data))
+                progress_step = 0.7/label_count
+
+                for i in range(label_count):
+                    if cancel():
+                        return
+
+                    name_i = f"{name}_{i+1}"
+                    progress = 0.2+i*progress_step
+                    progress_update(context, progress,
+                                    f"Processing {name_i}...")
+
+                    progress_callback = progress_callback_factory(name_i,
+                                                                  progress,
+                                                                  progress_step)
+                    try:
+                        layer = Layer(data=data == np.full_like(data, i+1),
+                                      name=name_i,
+                                      kind=kind,
+                                      affine=affine)
+
+                        layer.resize(shape=shape,
+                                     progress_callback=progress_callback)
+
+                        layers.append(layer)
+                    except CancelledByUser:
+                        return
+                    except Exception as e:
+                        self.has_error = e
+                        return
+
+            elif kind == "scalar":
+                name = self.layer_name or "Scalar"
+
+                if self.split_channels:
+                    progress_step = 0.7/self.channel_count
+
+                    for i in range(self.channel_count):
+                        if cancel():
+                            return
+
+                        name_i = f"{name}_{i+1}"
+                        progress = 0.2 + i*progress_step
+                        progress_update(context, progress,
+                                        f"Processing {name_i}...")
+                        progress_callback = progress_callback_factory(name_i,
+                                                                      progress,
+                                                                      progress_step)
+                        try:
+                            layer = Layer(data=data[:, :, :, :, i:i+1],
+                                          name=name_i,
+                                          kind=kind,
+                                          affine=affine)
+
+                            layer.resize(shape=shape,
+                                         progress_callback=progress_callback)
+
+                            layers.append(layer)
+                        except CancelledByUser:
+                            return
+                        except Exception as e:
+                            self.has_error = e
+                            return
+                else:
+                    if cancel():
+                        return
+
+                    progress_update(context, 0.2,
+                                    f"Processing {name}...")
+                    progress_callback = progress_callback_factory(name,
+                                                                  0.2,
+                                                                  0.7)
+
+                    try:
+                        layer = Layer(data=data,
+                                      name=name,
+                                      kind=kind,
+                                      affine=affine)
+
+                        layer.resize(shape=shape,
+                                     progress_callback=progress_callback)
+
+                        layers.append(layer)
+                    except CancelledByUser:
+                        return
+                    except Exception as e:
+                        self.has_error = e
+                        return
+
+            if cancel():
+                return
+
+            self.layers = layers
+            progress_update(context, 0.9, "Creating Layers...")
+
+        self.is_cancelled = False
+        self.has_error = None
+
+        self.thread = threading.Thread(target=import_volumetric_data_func,
+                                       args=(self, context, lambda: self.is_cancelled))
+
+        self.thread.start()
+        self._timer = context.window_manager.event_timer_add(time_step=0.1,
+                                                             window=context.window)
+        bpy.types.STATUSBAR_HT_header.append(progress_bar)
+
+        context.window_manager.modal_handler_add(self)
+        return {'RUNNING_MODAL'}
+
+    def modal(self, context, event):
+        if event.type == 'ESC':
+            self.is_cancelled = True
+            progress_update(context, 0, "Canceling...")
+            return {'PASS_THROUGH'}
+
+        if event.type != 'TIMER':
+            return {'PASS_THROUGH'}
+
+        bpy.context.workspace.status_text_set_internal(None)
+        if self.thread.is_alive():
+            return {'PASS_THROUGH'}
+
+        self.thread.join()
+        context.window_manager.event_timer_remove(self._timer)
+        bpy.types.STATUSBAR_HT_header.remove(progress_bar)
+
+        if self.is_cancelled:
+            self.report({"WARNING"}, "Canncelled by user.")
+            return {'CANCELLED'}
+
+        # Check if thread is cancelled by user
+        if self.has_error:
+            raise self.has_error
+
+        # Check if has return
+        if self.layers is None:
+            self.report({"ERROR"}, "Some thing went wrong.")
+            return {'CANCELLED'}
+
+        is_first_import = len(get_all_layer_objs()) == 0
+
+        if self.container_obj_name:
+            container_obj = bpy.data.objects.get(self.container_obj_name)
+            if container_obj is None:
+                raise Exception("Could not find target container")
+
+            container_obj = add_layers(self.layers,
+                                       container_obj=container_obj,
+                                       cache_dir=get_cache_dir(context))
+        else:
+            container = Container(name=self.container_name,
+                                  layers=self.layers)
+
+            container_obj = container_to_obj(container,
+                                             scene_scale=self.scene_scale,
+                                             cache_dir=get_cache_dir(context))
+
+        select_object(container_obj)
+
+        # Change render setting for better result
+        if is_first_import:
+            change_render_setting(context)
+
+        self.report({"INFO"}, "Successfully Imported")
+        return {'FINISHED'}
+
+    def invoke(self, context, event):
+        layer_kind = self.read_as.capitalize()
+        title = f"Add to **{self.container_obj_name}**, As {layer_kind}" \
+            if self.container_obj_name != "" else f"Init a Container, As {layer_kind}"
+        context.window_manager.invoke_props_dialog(self,
+                                                   width=500,
+                                                   title=title)
+        return {'RUNNING_MODAL'}
+
+    def draw(self, context):
+        layer_shape = get_layer_shape(self.bioxel_size,
+                                      self.orig_shape,
+                                      self.orig_spacing)
+
+        orig_shape = tuple(self.orig_shape)
+
+        # change shape as sequence or not
+        channel_count = self.channel_count
+        if self.sequence_source == "-1":
+            pass
+        elif self.sequence_source == "0":
+            # frame as frame
+            pass
+        elif self.sequence_source == "1":
+            layer_shape = (1, layer_shape[1], layer_shape[2])
+        elif self.sequence_source == "2":
+            layer_shape = (layer_shape[0], 1, layer_shape[2])
+        elif self.sequence_source == "3":
+            layer_shape = (layer_shape[0], layer_shape[1], 1)
+        else:
+            channel_count = 1
+
+        import_channel = channel_count if self.split_channels or channel_count == 1 else "combined"
+
+        bioxel_count = layer_shape[0] * layer_shape[1] * layer_shape[2]
+        layer_shape_text = f"Shape from {str(orig_shape)} to {str(layer_shape)}"
+        if bioxel_count > 100000000:
+            layer_shape_text += "**TOO LARGE!**"
+
+        layout = self.layout
+        if self.container_obj_name == "":
+            layout.prop(self, "container_name")
+        layout.prop(self, "layer_name")
+
+        panel = layout.box()
+        panel.prop(self, "bioxel_size")
+        row = panel.row()
+        row.prop(self, "orig_spacing")
+        panel.label(text=layer_shape_text)
+
+        panel = layout.box()
+        panel.prop(self, "sequence_source")
+
+        if self.read_as == "scalar":
+            panel = layout.box()
+            panel.prop(self, "split_channels",
+                       text=f"Split Channels (Get {channel_count} channels, import {import_channel} channels)")
+
+        if self.container_obj_name == "":
+            layer_size = get_layer_size(layer_shape,
+                                        self.bioxel_size,
+                                        self.scene_scale)
+            layer_size_text = f"Size will be: ({layer_size[0]:.2f}, {layer_size[1]:.2f}, {layer_size[2]:.2f}) m"
+            panel = layout.box()
+            panel.prop(self, "scene_scale")
+            panel.label(text=layer_size_text)
+
+
+class ExportVolumetricData(bpy.types.Operator):
+    bl_idname = "bioxelnodes.export_volumetric_data"
+    bl_label = "Export Layer as VDB"
+    bl_description = "Export Layer as VDB"
+    bl_options = {'UNDO'}
+
+    filepath: bpy.props.StringProperty(
+        subtype="FILE_PATH"
+    )  # type: ignore
+
+    filename_ext = ".vdb"
+
+    @classmethod
+    def poll(cls, context):
+        layer_obj = get_layer_obj(bpy.context.active_object)
+        return True if layer_obj else False
+
+    def invoke(self, context, event):
+        context.window_manager.fileselect_add(self)
+        return {'RUNNING_MODAL'}
+
+    def execute(self, context):
+        layer_obj = get_layer_obj(bpy.context.active_object)
+
+        filepath = f"{self.filepath.split('.')[0]}.vdb"
+        # "//"
+        source_dir = bpy.path.abspath(layer_obj.data.filepath)
+
+        output_path: Path = Path(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/operators/layer.py

@@ -0,0 +1,250 @@
+from pathlib import Path
+import bpy
+
+import numpy as np
+
+
+from ..bioxel.layer import Layer
+from ..bioxelutils.node import get_nodes_by_type
+from ..bioxelutils.container import add_layers, get_container_obj
+from ..bioxelutils.layer import obj_to_layer, get_container_layer_objs, get_layer_obj
+from .utils import get_preferences, select_object
+
+
+def get_layer_prop_value(layer_obj: bpy.types.Object, prop: str):
+    try:
+        node_group = layer_obj.modifiers[0].node_group
+        layer_node = get_nodes_by_type(node_group, "BioxelNodes__Layer")[0]
+        return layer_node.inputs[prop].default_value
+    except:
+        return None
+
+
+def get_label_layer_selection(self, context):
+    items = [("None", "None", "")]
+    container_obj = get_container_obj(bpy.context.active_object)
+
+    for layer_obj in get_container_layer_objs(container_obj):
+        if get_layer_prop_value(layer_obj, "kind") == "label":
+            items.append((layer_obj.name,
+                          layer_obj.name,
+                          ""))
+
+    return items
+
+
+class LayerOperator():
+    bl_options = {'UNDO'}
+    base_obj: bpy.types.Object = None
+
+    def add_layer(self, context, layer):
+        preferences = get_preferences(context)
+        cache_dir = Path(preferences.cache_dir, 'VDBs')
+        container_obj = self.base_obj.parent
+
+        add_layers([layer],
+                   container_obj,
+                   cache_dir)
+
+        select_object(container_obj)
+
+    def invoke(self, context, event):
+        self.base_obj = get_layer_obj(bpy.context.active_object)
+        return self.execute(context)
+
+
+class ScalarOperator(LayerOperator):
+    @classmethod
+    def poll(cls, context):
+        label_objs = [obj for obj in context.selected_ids
+                      if get_layer_prop_value(obj, "kind") == "scalar"]
+        return True if len(label_objs) > 0 else False
+
+
+class LabelOperator(LayerOperator):
+    @classmethod
+    def poll(cls, context):
+        label_objs = [obj for obj in context.selected_ids
+                      if get_layer_prop_value(obj, "kind") == "label"]
+        return True if len(label_objs) > 0 else False
+
+
+class SignScalar(bpy.types.Operator, ScalarOperator):
+    bl_idname = "bioxelnodes.sign_scalar"
+    bl_label = "Sign Scalar"
+    bl_description = "Sign the scalar value"
+
+    def execute(self, context):
+        base_layer = obj_to_layer(self.base_obj)
+
+        modified_layer = base_layer.copy()
+        modified_layer.data = -base_layer.data
+        modified_layer.name = f"{base_layer.name}_Signed"
+
+        self.add_layer(context, modified_layer)
+        return {'FINISHED'}
+
+
+class FillOperator(ScalarOperator):
+    def invoke(self, context, event):
+        self.base_obj = get_layer_obj(bpy.context.active_object)
+        scalar_min = get_layer_prop_value(self.base_obj, "min")
+        self.fill_value = min(scalar_min, 0)
+        context.window_manager.invoke_props_dialog(self, width=400)
+        return {'RUNNING_MODAL'}
+
+
+class FillByThreshold(bpy.types.Operator, FillOperator):
+    bl_idname = "bioxelnodes.fill_by_threshold"
+    bl_label = "Fill Value by Threshold"
+    bl_description = "Fill Value by Threshold"
+
+    threshold: bpy.props.FloatProperty(
+        name="Threshold",
+        soft_min=0, soft_max=1024,
+        default=128,
+    )  # type: ignore
+
+    fill_value: bpy.props.FloatProperty(
+        name="Fill Value",
+        soft_min=0, soft_max=1024.0,
+        default=0,
+    )  # type: ignore
+
+    invert: bpy.props.BoolProperty(
+        name="Invert Area",
+        default=True,
+    )  # type: ignore
+
+    def execute(self, context):
+        base_layer = obj_to_layer(self.base_obj)
+
+        data = np.amax(base_layer.data, -1)
+        mask = data <= self.threshold \
+            if self.invert else data > self.threshold
+
+        modified_layer = base_layer.copy()
+        modified_layer.fill(self.fill_value, mask)
+        modified_layer.name = f"{base_layer.name}_{self.threshold}-Filled"
+
+        self.add_layer(context, modified_layer)
+
+        return {'FINISHED'}
+
+
+class FillByRange(bpy.types.Operator, FillOperator):
+    bl_idname = "bioxelnodes.fill_by_range"
+    bl_label = "Fill Value by Range"
+    bl_description = "Fill Value by Range"
+
+    from_min: bpy.props.FloatProperty(
+        name="From Min",
+        soft_min=0, soft_max=1024,
+        default=128,
+    )  # type: ignore
+
+    from_max: bpy.props.FloatProperty(
+        name="From Max",
+        soft_min=0, soft_max=1024,
+        default=256,
+    )  # type: ignore
+
+    fill_value: bpy.props.FloatProperty(
+        name="Fill Value",
+        soft_min=0, soft_max=1024.0,
+        default=0,
+    )  # type: ignore
+
+    invert: bpy.props.BoolProperty(
+        name="Invert Area",
+        default=True,
+    )  # type: ignore
+
+    def execute(self, context):
+        base_layer = obj_to_layer(self.base_obj)
+
+        data = np.amax(base_layer.data, -1)
+        mask = (data <= self.from_min) | (data >= self.from_max) if self.invert else \
+            (data > self.from_min) & (data < self.from_max)
+
+        modified_layer = base_layer.copy()
+        modified_layer.fill(self.fill_value, mask)
+        modified_layer.name = f"{base_layer.name}_{self.from_min}-{self.from_max}-Filled"
+
+        self.add_layer(context, modified_layer)
+        return {'FINISHED'}
+
+
+class FillByLabel(bpy.types.Operator, FillOperator):
+    bl_idname = "bioxelnodes.fill_by_label"
+    bl_label = "Fill Value by Label"
+    bl_description = "Fill Value by Label Area"
+
+    label_obj_name: bpy.props.EnumProperty(
+        name="Label Layer",
+        items=get_label_layer_selection
+    )  # type: ignore
+
+    fill_value: bpy.props.FloatProperty(
+        name="Fill Value",
+        soft_min=0, soft_max=1024.0,
+        default=0,
+    )  # type: ignore
+
+    invert: bpy.props.BoolProperty(
+        name="Invert Label",
+        default=True,
+    )  # type: ignore
+
+    def execute(self, context):
+        label_obj = bpy.data.objects.get(self.label_obj_name)
+        if not label_obj:
+            self.report({"WARNING"}, "Cannot find any label layer.")
+            return {'FINISHED'}
+
+        base_layer = obj_to_layer(self.base_obj)
+
+        label_layer = obj_to_layer(label_obj)
+        label_layer.resize(base_layer.shape)
+        mask = np.amax(label_layer.data, -1)
+        if self.invert:
+            mask = 1 - mask
+
+        modified_layer = base_layer.copy()
+        modified_layer.fill(self.fill_value, mask)
+        modified_layer.name = f"{base_layer.name}_{label_layer.name}-Filled"
+
+        self.add_layer(context, modified_layer)
+        return {'FINISHED'}
+
+
+class CombineLabels(bpy.types.Operator, LabelOperator):
+    bl_idname = "bioxelnodes.combine_labels"
+    bl_label = "Combine Labels"
+    bl_description = "Combine all selected labels"
+
+    def execute(self, context):
+        label_objs = [obj for obj in context.selected_ids
+                      if get_layer_prop_value(obj, "kind") == "label"]
+
+        if len(label_objs) < 2:
+            self.report({"WARNING"}, "Not enough layers.")
+            return {'FINISHED'}
+        base_obj = label_objs[0]
+        label_objs = label_objs[1:]
+
+        base_layer = obj_to_layer(base_obj)
+        modified_layer = base_layer.copy()
+        label_names = [base_layer.name]
+
+        for label_obj in label_objs:
+            label_layer = obj_to_layer(label_obj)
+            label_layer.resize(base_layer.shape)
+            modified_layer.data = np.maximum(modified_layer.data, label_layer.data)
+            label_names.append(label_layer.name)
+
+        modified_layer.name = f"{'-'.join(label_names)}-Combined"
+
+        self.add_layer(context, modified_layer)
+
+        return {'FINISHED'}

bioxelnodes/operators/misc.py

@@ -2,8 +2,13 @@ import re
 import bpy
 from pathlib import Path
 import shutil
-from .utils import copy_to_dir, get_all_layers, get_container, get_container_from_selection, get_container_layers
+
-from .nodes import custom_nodes
+
+from ..utils import copy_to_dir
+from .utils import get_cache_dir
+from ..nodes import custom_nodes
+from ..bioxelutils.container import get_container_objs_from_selection
+from ..bioxelutils.layer import get_all_layer_objs, get_container_layer_objs
 
 CLASS_PREFIX = "BIOXELNODES_MT_NODES"
 
@@ -27,13 +32,37 @@ class ReLinkNodes(bpy.types.Operator):
         return {'FINISHED'}
 
 
+def save_layer_cache(layer_obj, output_dir):
+    pattern = r'\.\d{4}\.'
+
+    # "//"
+    output_dir = bpy.path.abspath(output_dir)
+    source_dir = bpy.path.abspath(layer_obj.data.filepath)
+
+    source_path: Path = Path(source_dir).resolve()
+    is_sequence = re.search(pattern, source_path.name) is not None
+    name = layer_obj.name if is_sequence else f"{layer_obj.name}.vdb"
+    output_path: Path = Path(output_dir, name, source_path.name).resolve() \
+        if is_sequence else Path(output_dir, name).resolve()
+
+    if output_path != source_path:
+        copy_to_dir(source_path.parent if is_sequence else source_path,
+                    output_path.parent.parent if is_sequence else output_path.parent,
+                    new_name=name)
+
+    blend_path = Path(bpy.path.abspath("//")).resolve()
+
+    layer_obj.data.filepath = bpy.path.relpath(
+        str(output_path), start=str(blend_path))
+
+
 class SaveStagedData(bpy.types.Operator):
     bl_idname = "bioxelnodes.save_staged_data"
     bl_label = "Save Staged Data"
     bl_description = "Save all staged data in this file for sharing"
 
-    save_layer: bpy.props.BoolProperty(
+    save_cache: bpy.props.BoolProperty(
-        name="Save Layer VDB Cache",
+        name="Save Layer Caches",
         default=True,
     )  # type: ignore
 
@@ -83,11 +112,11 @@ class SaveStagedData(bpy.types.Operator):
 
                 self.report({"INFO"}, f"Successfully saved to {output_path}")
 
-        if self.save_layer:
+        if self.save_cache:
             fails = []
-            for layer in get_all_layers():
+            for layer in get_all_layer_objs():
                 try:
-                    save_layer(layer, self.cache_dir)
+                    save_layer_cache(layer, self.cache_dir)
                 except:
                     fails.append(layer)
 
@@ -111,42 +140,17 @@ class SaveStagedData(bpy.types.Operator):
     def draw(self, context):
         layout = self.layout
         panel = layout.box()
-        panel.prop(self, "save_layer")
+        panel.prop(self, "save_cache")
         panel.prop(self, "cache_dir")
         panel = layout.box()
         panel.prop(self, "save_lib")
         panel.prop(self, "lib_dir")
 
 
-def save_layer(layer, output_dir):
+class SaveCaches(bpy.types.Operator):
-
+    bl_idname = "bioxelnodes.save_caches"
-    pattern = r'\.\d{4}\.'
+    bl_label = "Save Caches"
-
+    bl_description = "Save Container's caches to directory."
-    # "//"
-    output_dir = bpy.path.abspath(output_dir)
-    source_dir = bpy.path.abspath(layer.data.filepath)
-
-    source_path: Path = Path(source_dir).resolve()
-    is_sequence = re.search(pattern, source_path.name) is not None
-    name = layer.name if is_sequence else f"{layer.name}.vdb"
-    output_path: Path = Path(output_dir, name, source_path.name).resolve() \
-        if is_sequence else Path(output_dir, name).resolve()
-
-    if output_path != source_path:
-        copy_to_dir(source_path.parent if is_sequence else source_path,
-                    output_path.parent.parent if is_sequence else output_path.parent,
-                    new_name=name)
-
-    blend_path = Path(bpy.path.abspath("//")).resolve()
-
-    layer.data.filepath = bpy.path.relpath(
-        str(output_path), start=str(blend_path))
-
-
-class SaveLayers(bpy.types.Operator):
-    bl_idname = "bioxelnodes.save_layers"
-    bl_label = "Save Layers"
-    bl_description = "Save Container Layers to Directory."
 
     cache_dir: bpy.props.StringProperty(
         name="Layer Directory",
@@ -156,23 +160,23 @@ class SaveLayers(bpy.types.Operator):
 
     @classmethod
     def poll(cls, context):
-        containers = get_container_from_selection()
+        container_objs = get_container_objs_from_selection()
-        return len(containers) > 0
+        return len(container_objs) > 0
 
     def execute(self, context):
-        containers = get_container_from_selection()
+        container_objs = get_container_objs_from_selection()
 
-        if len(containers) == 0:
+        if len(container_objs) == 0:
             self.report({"WARNING"}, "Cannot find any bioxel container.")
             return {'FINISHED'}
 
         fails = []
-        for container in containers:
+        for container_obj in container_objs:
-            for layer in get_container_layers(container):
+            for layer_obj in get_container_layer_objs(container_obj):
                 try:
-                    save_layer(layer, self.cache_dir)
+                    save_layer_cache(layer_obj, self.cache_dir)
                 except:
-                    fails.append(layer)
+                    fails.append(layer_obj)
 
         if len(fails) == 0:
             self.report({"INFO"}, f"Successfully saved bioxel layers.")
@@ -194,8 +198,7 @@ class CleanAllCaches(bpy.types.Operator):
     bl_description = "Clean all caches saved in temp"
 
     def execute(self, context):
-        preferences = context.preferences.addons[__package__].preferences
+        cache_dir = get_cache_dir(context)
-        cache_dir = Path(preferences.cache_dir, 'VDBs')
         try:
             shutil.rmtree(cache_dir)
             self.report({"INFO"}, f"Successfully cleaned caches.")

bioxelnodes/operators/utils.py

@@ -0,0 +1,60 @@
+import bpy
+from pathlib import Path
+from .. import __package__ as base_package
+
+
+def change_render_setting(context):
+    preferences = get_preferences(context)
+    if preferences.do_change_render_setting:
+        bpy.context.scene.render.engine = 'CYCLES'
+        try:
+            bpy.context.scene.cycles.shading_system = True
+            bpy.context.scene.cycles.volume_bounces = 12
+            bpy.context.scene.cycles.transparent_max_bounces = 16
+            bpy.context.scene.cycles.volume_preview_step_rate = 10
+            bpy.context.scene.cycles.volume_step_rate = 10
+        except:
+            pass
+
+        try:
+            bpy.context.scene.eevee.use_taa_reprojection = False
+            bpy.context.scene.eevee.volumetric_tile_size = '2'
+            bpy.context.scene.eevee.volumetric_shadow_samples = 128
+            bpy.context.scene.eevee.volumetric_samples = 256
+            bpy.context.scene.eevee.use_volumetric_shadows = True
+        except:
+            pass
+
+
+def select_object(target_obj):
+    for obj in bpy.data.objects:
+        obj.select_set(False)
+
+    target_obj.select_set(True)
+    bpy.context.view_layer.objects.active = target_obj
+
+
+def progress_bar(self, context):
+    row = self.layout.row()
+    row.progress(
+        factor=context.window_manager.bioxelnodes_progress_factor,
+        type="BAR",
+        text=context.window_manager.bioxelnodes_progress_text
+    )
+    row.scale_x = 2
+
+
+def progress_update(context, factor, text=""):
+    context.window_manager.bioxelnodes_progress_factor = factor
+    context.window_manager.bioxelnodes_progress_text = text
+
+
+def get_preferences(context):
+    return context.preferences.addons[base_package].preferences
+
+
+def get_cache_dir(context):
+    preferences = get_preferences(context)
+    cache_path = Path(preferences.cache_dir, 'VDBs')
+    cache_path.mkdir(parents=True, exist_ok=True)
+    return str(cache_path)

bioxelnodes/preferences.py

@@ -1,9 +1,7 @@
 import bpy
 from pathlib import Path
-from .externalpackage import ExternalPackagePreferences
 
-
+class BioxelNodesPreferences(bpy.types.AddonPreferences):
-class BioxelNodesPreferences(bpy.types.AddonPreferences, ExternalPackagePreferences):
     bl_idname = __package__
 
     cache_dir: bpy.props.StringProperty(
@@ -20,10 +18,6 @@ class BioxelNodesPreferences(bpy.types.AddonPreferences, ExternalPackagePreferen
     def draw(self, context):
         layout = self.layout
 
-        # ExternalPackagePreferences Config
-        self.requirements_dir = str(Path(__file__).parent)
-        super().draw(context)
-
         layout.label(text="Configuration")
         layout.prop(self, 'cache_dir')
         layout.prop(self, "do_change_render_setting")

bioxelnodes/requirements.txt

@@ -1 +0,0 @@
-SimpleITK==2.3.1     # Insight Segmentation and Registration Toolkit.

bioxelnodes/scipy/__init__.py

@@ -1,2 +0,0 @@
-from ._interpolation import zoom
-from ._filters import gaussian_filter, median_filter

bioxelnodes/utils.py

@@ -1,19 +1,7 @@
-import bpy
-import mathutils
 from pathlib import Path
-import pyopenvdb as vdb
-from uuid import uuid4
 import shutil
 
 
-def select_object(target_obj):
-    for obj in bpy.data.objects:
-        obj.select_set(False)
-
-    target_obj.select_set(True)
-    bpy.context.view_layer.objects.active = target_obj
-
-
 def copy_to_dir(source_path, dir_path, new_name=None, exist_ok=True):
     source = Path(source_path)
     target = Path(dir_path)
@@ -42,246 +30,3 @@ def copy_to_dir(source_path, dir_path, new_name=None, exist_ok=True):
 
     if not target_path.exists():
         raise Exception
-
-
-def move_node_to_node(node, target_node, offset=(0, 0)):
-    node.location.x = target_node.location.x + offset[0]
-    node.location.y = target_node.location.y + offset[1]
-
-
-def move_node_between_nodes(node, target_nodes, offset=(0, 0)):
-    xs = []
-    ys = []
-    for target_node in target_nodes:
-        xs.append(target_node.location.x)
-        ys.append(target_node.location.y)
-
-    node.location.x = sum(xs) / len(xs) + offset[0]
-    node.location.y = sum(ys) / len(ys) + offset[1]
-
-
-def get_node_type(node):
-    node_type = type(node).__name__
-    if node_type == "GeometryNodeGroup":
-        node_type = node.node_tree.name
-
-    return node_type
-
-
-def get_nodes_by_type(node_group, type_name: str):
-    return [node for node in node_group.nodes if get_node_type(node) == type_name]
-
-
-def show_message(message="", title="Message Box", icon='INFO'):
-
-    def draw(self, context):
-        self.layout.label(text=message)
-
-    bpy.context.window_manager.popup_menu(draw, title=title, icon=icon)
-
-
-def calc_bbox_verts(origin, size):
-    bbox_origin = mathutils.Vector(
-        (origin[0], origin[1], origin[2]))
-    bbox_size = mathutils.Vector(
-        (size[0], size[1], size[2]))
-    bbox_verts = [
-        (
-            bbox_origin[0] + 0,
-            bbox_origin[1] + 0,
-            bbox_origin[2] + 0
-        ),
-        (
-            bbox_origin[0] + 0,
-            bbox_origin[1] + 0,
-            bbox_origin[2] + bbox_size[2]
-        ),
-        (
-            bbox_origin[0] + 0,
-            bbox_origin[1] + bbox_size[1],
-            bbox_origin[2] + 0
-        ),
-        (
-            bbox_origin[0] + 0,
-            bbox_origin[1] + bbox_size[1],
-            bbox_origin[2] + bbox_size[2]
-        ),
-        (
-            bbox_origin[0] + bbox_size[0],
-            bbox_origin[1] + 0,
-            bbox_origin[2] + 0
-        ),
-        (
-            bbox_origin[0] + bbox_size[0],
-            bbox_origin[1] + 0,
-            bbox_origin[2] + bbox_size[2],
-        ),
-        (
-            bbox_origin[0] + bbox_size[0],
-            bbox_origin[1] + bbox_size[1],
-            bbox_origin[2] + 0,
-        ),
-        (
-            bbox_origin[0] + bbox_size[0],
-            bbox_origin[1] + bbox_size[1],
-            bbox_origin[2] + bbox_size[2],
-        ),
-    ]
-    return bbox_verts
-
-
-def lock_transform(obj):
-    obj.lock_location[0] = True
-    obj.lock_location[1] = True
-    obj.lock_location[2] = True
-    obj.lock_rotation[0] = True
-    obj.lock_rotation[1] = True
-    obj.lock_rotation[2] = True
-    obj.lock_scale[0] = True
-    obj.lock_scale[1] = True
-    obj.lock_scale[2] = True
-
-
-def hide_in_ray(obj):
-    obj.visible_camera = False
-    obj.visible_diffuse = False
-    obj.visible_glossy = False
-    obj.visible_transmission = False
-    obj.visible_volume_scatter = False
-    obj.visible_shadow = False
-
-
-def save_vdb(grids, context):
-    preferences = context.preferences.addons[__package__].preferences
-    cache_dir = Path(preferences.cache_dir, 'VDBs')
-    cache_dir.mkdir(parents=True, exist_ok=True)
-
-    vdb_path = Path(cache_dir, f"{uuid4()}.vdb")
-    print(f"Storing the VDB file ({str(vdb_path)})...")
-    vdb.write(str(vdb_path), grids=grids)
-
-    return vdb_path
-
-
-def save_vdbs(grids_sequence, context):
-    preferences = context.preferences.addons[__package__].preferences
-    cache_dir = Path(preferences.cache_dir, 'VDBs')
-    cache_dir.mkdir(parents=True, exist_ok=True)
-    vdb_name = str(uuid4())
-    vdb_dir_path = Path(cache_dir, vdb_name)
-    vdb_dir_path.mkdir(parents=True, exist_ok=True)
-
-    vdb_paths = []
-    for f, grids in enumerate(grids_sequence):
-        vdb_path = Path(vdb_dir_path, f"{vdb_name}.{str(f+1).zfill(4)}.vdb")
-        print(f"Storing the VDB file ({str(vdb_path)})...")
-        vdb.write(str(vdb_path), grids=grids)
-        vdb_paths.append(vdb_path)
-
-    return vdb_paths
-
-
-def get_container_from_selection():
-    containers = []
-    for obj in bpy.context.selected_objects:
-        if get_container(obj):
-            containers.append(obj)
-    # if bpy.context.active_object:
-    #     if bpy.context.active_object.get('bioxel_layer'):
-    #         if bpy.context.active_object.parent.get('bioxel_container'):
-    #             containers.append(bpy.context.active_object.parent)
-
-    return list(set(containers))
-
-
-def get_container(current_obj):
-    if current_obj:
-        if current_obj.get('bioxel_container'):
-            return current_obj
-        elif current_obj.get('bioxel_layer'):
-            parent = current_obj.parent
-            return parent if parent.get('bioxel_container') else None
-    return None
-
-
-def get_layer(current_obj):
-    if current_obj:
-        if current_obj.get('bioxel_layer') and current_obj.parent:
-            if current_obj.parent.get('bioxel_container'):
-                return current_obj
-    return None
-
-
-def get_container_layers(container):
-    layers = []
-    for obj in bpy.data.objects:
-        if obj.parent == container and get_layer(obj):
-            layers.append(obj)
-
-    return layers
-
-
-def get_all_layers():
-    layers = []
-    for obj in bpy.data.objects:
-        if get_layer(obj):
-            layers.append(obj)
-
-    return layers
-
-
-def get_text_index_str(text):
-    # Initialize an empty string to store the digits
-    digits = ""
-
-    # Iterate through the characters in reverse order
-    started = False
-    for char in text[::-1]:
-        if char.isdigit():
-            started = True
-            # If the character is a digit, add it to the digits string
-            digits += char
-        else:
-            if started:
-                # If a non-digit character is encountered, stop the loop
-                break
-
-    # Reverse the digits string to get the correct order
-    last_number = digits[::-1]
-
-    return last_number
-
-
-def add_driver(target_prop, var_sources, expression):
-
-    driver = target_prop.driver_add("default_value")
-    is_vector = isinstance(driver, list)
-    drivers = driver if is_vector else [driver]
-
-    for i, driver in enumerate(drivers):
-        for j, var_source in enumerate(var_sources):
-
-            source = var_source['source']
-            prop = var_source['prop']
-
-            var = driver.driver.variables.new()
-            var.name = f"var{j}"
-
-            var.targets[0].id_type = source.id_type
-            var.targets[0].id = source
-            var.targets[0].data_path = f'["{prop}"][{i}]'\
-                if is_vector else f'["{prop}"]'
-
-        driver.driver.expression = expression
-
-
-def add_direct_driver(target, target_prop, source, source_prop):
-    target_prop = target.inputs.get(target_prop)
-    drivers = [
-        {
-            "source": source,
-            "prop": source_prop
-        }
-    ]
-    expression = "var0"
-    add_driver(target_prop, drivers, expression)

build.py

@@ -0,0 +1,95 @@
+from pathlib import Path
+import shutil
+import subprocess
+import sys
+from dataclasses import dataclass
+import tomlkit
+
+
+@dataclass
+class Platform:
+    pypi_suffix: str
+    blender_tag: str
+
+
+required_packages = ["SimpleITK==2.3.1",
+                     "pyometiff==1.0.0",
+                     "mrcfile==1.5.1",
+                     "h5py==3.11.0",
+                     "transforms3d==0.4.2"]
+
+
+platforms = {"windows-x64": Platform(pypi_suffix="win_amd64",
+                                     blender_tag="windows-x64"),
+             "linux-x64": Platform(pypi_suffix="manylinux2014_x86_64",
+                                   blender_tag="linux-x64"),
+             "macos-arm64": Platform(pypi_suffix="macosx_12_0_arm64",
+                                     blender_tag="macos-arm64"),
+             "macos-x64": Platform(pypi_suffix="macosx_10_16_x86_64",
+                                   blender_tag="macos-x64")}
+
+packages_to_remove = {
+    "imagecodecs",
+    "numpy"
+}
+
+
+def run_python(args: str):
+    python = Path(sys.executable).resolve()
+    subprocess.run([python] + args.split(" "))
+
+
+def build_extension(platform: Platform, python_version="3.11") -> None:
+    wheel_dirpath = Path("./bioxelnodes/wheels")
+    toml_filepath = Path("bioxelnodes/blender_manifest.toml")
+    scipy_ndimage_dirpath = Path("./scipy_ndimage", platform.blender_tag)
+
+    # download required_packages
+    run_python(
+        f"-m pip download {' '.join(required_packages)} --dest {wheel_dirpath.as_posix()} --only-binary=:all: --python-version={python_version} --platform={platform.pypi_suffix}"
+    )
+
+    for f in wheel_dirpath.glob('*.whl'):
+        if any([package in f.name for package in packages_to_remove]):
+            f.unlink(missing_ok=True)
+
+        elif platform.blender_tag == "macos-arm64" and \
+                "lxml" in f.name and "universal2" in f.name:
+            f.rename(Path(f.parent,
+                          f.name.replace("universal2", "arm64")))
+
+    for ndimage_filepath in scipy_ndimage_dirpath.iterdir():
+        to_filepath = Path("./bioxelnodes/bioxel/scipy", ndimage_filepath.name)
+        shutil.copy(ndimage_filepath, to_filepath)
+
+    # Load the TOML file
+    with toml_filepath.open("r") as file:
+        manifest = tomlkit.parse(file.read())
+
+    manifest["platforms"] = [platform.blender_tag]
+    manifest["wheels"] = [f"./wheels/{f.name}"
+                          for f in wheel_dirpath.glob('*.whl')]
+
+    # build = tomlkit.table(True)
+    # generated = tomlkit.table()
+    # generated["platforms"] = [platform.blender_tag]
+    # generated["wheels"] = [f"./wheels/{f.name}"
+    #                        for f in wheel_dirpath.glob('*.whl')]
+
+    # build.append('generated', generated)
+    # manifest.append('build', build)
+
+    # Write the updated TOML file
+    with toml_filepath.open("w") as file:
+        text = tomlkit.dumps(manifest)
+        file.write(text)
+
+
+def main():
+    platform_name = sys.argv[1]
+    platform = platforms[platform_name]
+    build_extension(platform)
+
+
+if __name__ == "__main__":
+    main()

docs/index.md

@@ -1,23 +1,34 @@
+[中文文档](https://uj6xfhbzp0.feishu.cn/wiki/Qx3VwHuNPimeI8kr6nDcvl1DnHf?from=from_copylink)
+
 # Bioxel Nodes
 
+[![For Blender](https://img.shields.io/badge/Blender-orange?style=for-the-badge&logo=blender&logoColor=white&color=black)](https://blender.org/)
+![GitHub License](https://img.shields.io/github/license/OmooLab/BioxelNodes?style=for-the-badge&labelColor=black)
+![GitHub Release](https://img.shields.io/github/v/release/OmooLab/BioxelNodes?style=for-the-badge&labelColor=black)
+![GitHub Repo stars](https://img.shields.io/github/stars/OmooLab/BioxelNodes?style=for-the-badge&labelColor=black)
+
+[![Discord](https://img.shields.io/discord/1265129134397587457?style=for-the-badge&logo=discord&label=Discord&labelColor=white&color=black)](https://discord.gg/pYkNyq2TjE)
+
 Bioxel Nodes is a Blender addon for scientific volumetric data visualization. It using Blender's powerful **Geometry Nodes** and **Cycles** to process and render volumetric data.
 
-![cover](assets/cover.png)
+![cover](https://omoolab.github.io/BioxelNodes/latest/assets/cover.png)
 
--   Fantastic rendering result, also support EEVEE NEXT
+-   Realistic rendering result, also support EEVEE NEXT.
--   Support multiple formats
+-   Support multiple formats.
--   Support 4D volumetric data
+-   Support 4D volumetric data.
--   All kinds of cutters
+-   All kinds of cutters.
--   Simple and powerful nodes
+-   Simple and powerful nodes.
 -   Based on blender natively, can work without addon.
 
-**Click [Getting Started](https://omoolab.github.io/BioxelNodes/latest/installation) to begin your journey into visualizing volumetric data!**
+**Read the [getting started](https://omoolab.github.io/BioxelNodes/latest/installation) to begin your journey into visualizing volumetric data!**
+
+Welcome to our [discord server](https://discord.gg/pYkNyq2TjE), if you have any problems with this add-on.
 
 ## Support Multiple Formats
 
 | Format | EXT                                      | Test    |
 | ------ | ---------------------------------------- | ------- |
-| DICOM  | .dcm, .DICOM                             | ✅ pass |
+| DICOM  | .dcm, .DCM, .DICOM, .ima, .IMA           | ✅ pass |
 | BMP    | .bmp, .BMP                               | ✅ pass |
 | JPEG   | .jpg, .JPG, .jpeg, .JPEG                 | ✅ pass |
 | PNG    | .png, .PNG                               | ✅ pass |
@@ -25,16 +36,18 @@ Bioxel Nodes is a Blender addon for scientific volumetric data visualization. It
 | Nifti  | .nia, .nii, .nii.gz, .hdr, .img, .img.gz | ✅ pass |
 | Nrrd   | .nrrd, .nhdr                             | ✅ pass |
 | HDF5   | .hdf, .h4, .hdf4, .he2, .h5, .hdf5, .he5 | ✅ pass |
+| OME    | .ome.tiff, .ome.tif                      | ✅ pass |
+| MRC    | .mrc, .mrc.gz, .map, .map.gz             | ✅ pass |
 
 ## Support 4D volumetric data
 
-![4d](assets/4d-time.gif)
+![4d](https://omoolab.github.io/BioxelNodes/latest/assets/4d-time.gif)
 
 🥰 4D volumetric data can also be imported into Blender.
 
 ## Support EEVEE NEXT
 
-![eevee](assets/eevee.gif)
+![eevee](https://omoolab.github.io/BioxelNodes/latest/assets/eevee.gif)
 
 👍 EEVEE NEXT is absolutely AWESOME! Bioxel Nodes is fully support EEVEE NEXT now! However, there are some limitations:
 
@@ -46,17 +59,18 @@ Bioxel Nodes is a Blender addon for scientific volumetric data visualization. It
 -   Only works with Cycles CPU , Cycles GPU (OptiX), EEVEE
 -   Section surface cannot be generated when convert to mesh (will be supported soon)
 
-## Compatibile to Newer Version
+## Compatible to Newer Version
 
-**Updating this addon may break old files, so read the following carefully before updating**
+**v0.3.x is not compatible to v0.2.x, Updating this addon may break old files. Read the following carefully before upgradation**
 
-Before updating this addon, you need to ask yourself whether this project file will be modified again or not, if it's an archived project file, I would recommend that you run **Bioxel Nodes > Save Staged Data** to make the addon nodes permanent. In this way, there will be no potential problem with the nodes not functioning due to the addon update.
+Before upgradation, you need to ask yourself whether this project file will be modified again or not, if it's an archived project file, I would recommend that you run **Bioxel Nodes > Save Staged Data** to make the addon nodes permanent. In this way, there will be no potential problem with the nodes not functioning due to the addon update.
 
 After the addon update, your old project files may not work either, this may be because you had executed **Save Staged Data**. If so, you need to execute **Bioxel Nodes > Relink Nodes to Addon** to relink them to make sure that the addon's new functionality and the addon nodes are synchronized.
 
-Also, unlike the newer versions, the older shaders are not based on OSL, so if you find that you can't render volumes, you need to turn on **Open Shading Language (OSL)** in the Render Settings.
+Also, the older shaders are not based on OSL, so if you find that you can't render volumes, you need to turn on **Open Shading Language (OSL)** in the Render Settings.
 
 ## Roadmap
+
 -   Better multi-format import experience
 -   One-click bake model with texture
 -   AI Segmentation to Generate Labels

docs/prepare_data.md

@@ -6,7 +6,7 @@ First thing first, you need to get your volumetric data ready in disk. Bioxel No
 
 | Format | EXT                                      | Test    |
 | ------ | ---------------------------------------- | ------- |
-| DICOM  | .dcm, .DICOM                             | ✅ pass |
+| DICOM  | .dcm, .DCM, .DICOM, .ima, .IMA           | ✅ pass |
 | BMP    | .bmp, .BMP                               | ✅ pass |
 | JPEG   | .jpg, .JPG, .jpeg, .JPEG                 | ✅ pass |
 | PNG    | .png, .PNG                               | ✅ pass |
@@ -21,6 +21,8 @@ First thing first, you need to get your volumetric data ready in disk. Bioxel No
 | LSM    | .lsm, .LSM                               | yet     |
 | MINC   | .mnc, .MNC                               | yet     |
 | MRC    | .mrc, .rec                               | yet     |
+| OME    | .ome.tiff, .ome.tif                      | ✅ pass |
+| MRC    | .mrc, .mrc.gz, .map, .map.gz             | ✅ pass |
 
 ## Download Data from Internet
 
@@ -32,10 +34,12 @@ If you don't have any volumetric data, you can access open research data from li
 | ------------------------------------------------------------------------------------ | ------------------ |
 | [MorphoSource](https://www.morphosource.org/)                                        | Open Research Data |
 | [Dryad](https://datadryad.org)                                                       | Open Research Data |
+| [Cell Image Library](http://cellimagelibrary.org/home)                               | Cells              |
 | [OpenOrganelle](https://openorganelle.janelia.org/datasets)                          | Cells              |
+| [Allen Cell Explorer](https://www.allencell.org/3d-cell-viewer.html)                 | Cells              |
+| [EMDB](https://www.ebi.ac.uk/emdb/)                                                  | Protein, Viruses   |
 | [Embodi3D](https://www.embodi3d.com/files/category/37-medical-scans/)                | Medical Images     |
 | [Github](https://github.com/sfikas/medical-imaging-datasets)                         | Medical Images     |
 | [NIHR](https://nhsx.github.io/open-source-imaging-data-sets/)                        | Medical Images     |
 | [Medical Segmentation Decathlon](http://medicaldecathlon.com/)                       | Medical Images     |
-| [Allen Cell Explorer](https://www.allencell.org/3d-cell-viewer.html)                 | Cells              |
 | [Visible Human Project](https://www.nlm.nih.gov/research/visible/visible_human.html) | Medical Images     |

extension/__init__.py

@@ -1,17 +0,0 @@
-import bpy
-
-from . import auto_load
-from . import menus
-
-
-auto_load.init()
-
-
-def register():
-    auto_load.register()
-    menus.add()
-
-
-def unregister():
-    menus.remove()
-    auto_load.unregister()

extension/blender_manifest.toml

@@ -1,69 +0,0 @@
-schema_version = "1.0.0"
-
-# Example of manifest file for a Blender extension
-# Change the values according to your extension
-id = "bioxelnodes"
-version = "0.2.7"
-name = "Bioxel Nodes"
-tagline = "For scientific volumetric data visualization in Blender"
-maintainer = "Ma Nan <icrdr2010@outlook.com>"
-# Supported types: "add-on", "theme"
-type = "add-on"
-
-# Optional link to documentation, support, source files, etc
-website = "https://omoolab.github.io/BioxelNodes/latest"
-
-# Optional list defined by Blender and server, see:
-# https://docs.blender.org/manual/en/dev/advanced/extensions/tags.html
-tags = ["Geometry Nodes", "Render"]
-
-blender_version_min = "4.2.0"
-# Optional: maximum supported Blender version
-# blender_version_max = "5.1.0"
-
-# License conforming to https://spdx.org/licenses/ (use "SPDX: prefix)
-# https://docs.blender.org/manual/en/dev/advanced/extensions/licenses.html
-license = [
-  "SPDX:MIT",
-]
-# Optional: required by some licenses.
-copyright = [
-  "2024 OmooLab"
-]
-
-# Optional list of supported platforms. If omitted, the extension will be available in all operating systems.
-platforms = ["windows-x64"]
-# Other supported platforms: "windows-arm64", "macos-x64"
-
-# Optional: bundle 3rd party Python modules.
-# https://docs.blender.org/manual/en/dev/advanced/extensions/python_wheels.html
-wheels = [
-  "./wheels/SimpleITK-2.3.1-cp311-cp311-win_amd64.whl"
-]
-
-
-## Optional: add-ons can list which resources they will require:
-## * files (for access of any filesystem operations)
-## * network (for internet access)
-## * clipboard (to read and/or write the system clipboard)
-## * camera (to capture photos and videos)
-## * microphone (to capture audio)
-##
-## If using network, remember to also check `bpy.app.online_access`
-## https://docs.blender.org/manual/en/dev/advanced/extensions/addons.html#internet-access
-##
-## For each permission it is important to also specify the reason why it is required.
-## Keep this a single short sentence without a period (.) at the end.
-## For longer explanations use the documentation or detail page.
-#
-[permissions]
-files = "Import/export volume data from/to disk"
-
-# Optional: build settings.
-# https://docs.blender.org/manual/en/dev/advanced/extensions/command_line_arguments.html#command-line-args-extension-build
-# [build]
-# paths_exclude_pattern = [
-#   "__pycache__/",
-#   "/.git/",
-#   "/*.zip",
-# ]

extension/preferences.py

@@ -1,23 +0,0 @@
-import bpy
-from pathlib import Path
-
-class BioxelNodesPreferences(bpy.types.AddonPreferences):
-    bl_idname = __package__
-
-    cache_dir: bpy.props.StringProperty(
-        name="Set Cache Directory",
-        subtype='DIR_PATH',
-        default=str(Path(Path.home(), '.bioxelnodes'))
-    )  # type: ignore
-
-    do_change_render_setting: bpy.props.BoolProperty(
-        name="Change Render Setting",
-        default=True,
-    )  # type: ignore
-
-    def draw(self, context):
-        layout = self.layout
-
-        layout.label(text="Configuration")
-        layout.prop(self, 'cache_dir')
-        layout.prop(self, "do_change_render_setting")

mkdocs.yml

@@ -13,7 +13,7 @@ nav:
       - Prepare Your Data: prepare_data.md
       - Step by Step: step_by_step.md
       - Concepts & Pipeline: concept.md
-  - Visualizating any Bio-structure:
+  - Visualizing any Bio-structure:
       - Import & Preprocess: import.md
       - Mask Methods: mask.md
       - Assgin a Shader: shader.md

pyproject.toml

@@ -1,29 +1,29 @@
 [tool.poetry]
 name = "bioxelnodes"
-version = "0.2.7"
+version = "0.3.3"
 description = ""
 authors = ["Ma Nan <icrdr2010@outlook.com>"]
 license = "MIT"
 readme = "README.md"
 
 [tool.poetry.dependencies]
-python = "~=3.10.0"
+python = ">=3.11.0,<3.12.dev0"
-bpy = "~=4.0"
+simpleitk = "2.3.1"
-simpleitk = "^2.3.1"
+pyometiff = "1.0.0"
-scikit-image = "^0.24.0"
+mrcfile = "1.5.1"
+h5py = "3.11.0"
+transforms3d = "0.4.2"
 
 [tool.poetry.group.dev.dependencies]
-ipykernel = "^6.25.2"
+bpy = "^4.2.0"
-pytest = "^7.4.2"
+pytest = "^8.3.2"
-pytest-dependency = "^0.5.1"
+pytest-dependency = "^0.6.0"
-mkdocs = "^1.5.3"
+pytest-cov = "^5.0.0"
-mkdocs-material = "^9.4.6"
+mkdocs = "^1.6.0"
-mkdocstrings = { extras = ["python"], version = "^0.23.0" }
+mkdocs-material = "^9.5.30"
-mkdocs-click = "^0.8.1"
+autopep8 = "^2.3.1"
-autopep8 = "^2.0.4"
+mike = "^2.1.2"
-pytest-cov = "^4.1.0"
+tomlkit = "^0.13.0"
-mike = "^2.0.0"
-
 
 [build-system]
 requires = ["poetry-core"]

requirements.txt

@@ -0,0 +1,5 @@
+SimpleITK==2.3.1     # Insight Segmentation and Registration Toolkit.
+pyometiff==1.0.0     # .ome.tiff
+mrcfile==1.5.1       # .map
+h5py==3.11.0         # .h5
+transforms3d==0.4.2  # transforms