Merge pull request #49 from OmooLab/feature/dev

feat: improve eevee render

.gitignore

@@ -133,4 +133,6 @@ blendcache_*
 
 .secrets
 
+.vdb
+
 !scipy_ndimage/*/**

README.md

@@ -1,4 +1,4 @@
-[中文文档](https://uj6xfhbzp0.feishu.cn/wiki/Qx3VwHuNPimeI8kr6nDcvl1DnHf?from=from_copylink)
+[中文文档](https://uj6xfhbzp0.feishu.cn/wiki/LPKEwjooSivxjskWHlCcQznjnNf?from=from_copylink)
 
 # Bioxel Nodes
 
@@ -26,18 +26,18 @@ Welcome to our [discord server](https://discord.gg/pYkNyq2TjE), if you have any
 
 ## Support Multiple Formats
 
-| Format | EXT                                      | Test    |
+| Format | EXT                                      |
-| ------ | ---------------------------------------- | ------- |
+| ------ | ---------------------------------------- |
-| DICOM  | .dcm, .DCM, .DICOM, .ima, .IMA           | ✅ pass |
+| DICOM  | .dcm, .DCM, .DICOM, .ima, .IMA           |
-| BMP    | .bmp, .BMP                               | ✅ pass |
+| BMP    | .bmp, .BMP                               |
-| JPEG   | .jpg, .JPG, .jpeg, .JPEG                 | ✅ pass |
+| JPEG   | .jpg, .JPG, .jpeg, .JPEG                 |
-| PNG    | .png, .PNG                               | ✅ pass |
+| PNG    | .png, .PNG                               |
-| TIFF   | .tif, .TIF, .tiff, .TIFF                 | ✅ pass |
+| TIFF   | .tif, .TIF, .tiff, .TIFF                 |
-| Nifti  | .nia, .nii, .nii.gz, .hdr, .img, .img.gz | ✅ pass |
+| Nifti  | .nia, .nii, .nii.gz, .hdr, .img, .img.gz |
-| Nrrd   | .nrrd, .nhdr                             | ✅ pass |
+| Nrrd   | .nrrd, .nhdr                             |
-| HDF5   | .hdf, .h4, .hdf4, .he2, .h5, .hdf5, .he5 | ✅ pass |
+| HDF5   | .hdf, .h4, .hdf4, .he2, .h5, .hdf5, .he5 |
-| OME    | .ome.tiff, .ome.tif                      | ✅ pass |
+| OME    | .ome.tiff, .ome.tif                      |
-| MRC    | .mrc, .mrc.gz, .map, .map.gz             | ✅ pass |
+| MRC    | .mrc, .mrc.gz, .map, .map.gz             |
 
 ## Support 4D volumetric data
 
@@ -59,16 +59,6 @@ Welcome to our [discord server](https://discord.gg/pYkNyq2TjE), if you have any
 -   Only works with Cycles CPU , Cycles GPU (OptiX), EEVEE
 -   Section surface cannot be generated when convert to mesh (will be supported soon)
 
-## Compatible to Newer Version
-
-**v0.3.x is not compatible to v0.2.x, Updating this addon may break old files. Read the following carefully before upgradation**
-
-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, 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

bioxelnodes/__init__.py

@@ -1,5 +1,6 @@
 import bpy
 
+from .props import BIOXELNODES_LayerListUL
 from . import auto_load
 from . import menus
 
@@ -9,11 +10,17 @@ auto_load.init()
 
 def register():
     auto_load.register()
-    bpy.types.WindowManager.bioxelnodes_progress_factor = bpy.props.FloatProperty()
+    bpy.types.WindowManager.bioxelnodes_progress_factor = bpy.props.FloatProperty(
+        default=1.0)
     bpy.types.WindowManager.bioxelnodes_progress_text = bpy.props.StringProperty()
+    bpy.types.WindowManager.bioxelnodes_layer_list_UL = bpy.props.PointerProperty(
+        type=BIOXELNODES_LayerListUL)
     menus.add()
 
 
 def unregister():
     menus.remove()
+    del bpy.types.WindowManager.bioxelnodes_progress_factor
+    del bpy.types.WindowManager.bioxelnodes_progress_text
+    del bpy.types.WindowManager.bioxelnodes_layer_list_UL
     auto_load.unregister()

bioxelnodes/bioxel/layer.py

@@ -2,11 +2,10 @@ 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
 
 
@@ -70,23 +69,27 @@ class Layer():
     def copy(self):
         return copy.deepcopy(self)
 
-    def fill(self, value: float, mask: np.ndarray):
+    def fill(self, value: float, mask: np.ndarray, smooth: int = 0):
         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(
+                if smooth > 0:
-                    mask_frame.astype(np.float32), size=3)
+                    mask_frame = scipy.median_filter(mask_frame.astype(np.float32),
+                                                      mode="nearest",
+                                                      size=smooth)
                 # 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(
+                if smooth > 0:
-                    mask_frame.astype(np.float32), size=3)
+                    mask_frame = scipy.median_filter(mask_frame.astype(np.float32),
+                                                      mode="nearest",
+                                                      size=smooth)
                 # mask_frame = scipy.median_filter(
                 #     mask_frame.astype(np.float32), size=2)
                 mask_frames += (mask_frame,)
@@ -97,39 +100,53 @@ class Layer():
         _mask = np.expand_dims(_mask, axis=-1)
         self.data = _mask * value + (1-_mask) * self.data
 
-    def resize(self, shape:tuple, progress_callback=None):
+    def resize(self, shape: tuple, smooth: int = 0, progress_callback=None):
         if len(shape) != 3:
             raise Exception("Shape must be 3 dim")
 
         data = self.data
 
-        # TXYZC > TXYZ
+        # # TXYZC > TXYZ
-        if self.kind in ['label', 'scalar']:
+        # if self.kind in ['label', 'scalar']:
-            data = np.amax(data, -1)
+        #     data = np.amax(data, -1)
 
-        if self.kind in ['scalar']:
+        # if self.kind in ['scalar']:
-            dtype = data.dtype
+        #     dtype = data.dtype
-            data = data.astype(np.float32)
+        # 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, :, :, :],
+            frame = data[f, :, :, :, :]
-                               shape,
+            if smooth > 0:
-                               preserve_range=True,
+                frame = scipy.median_filter(frame.astype(np.float32),
-                               anti_aliasing=data.dtype.kind != "b")
+                                            mode="nearest",
+                                            size=smooth)
 
+            factors = np.divide(self.shape, shape)
+            zoom_factors = [1 / f for f in factors]
+            order = 0 if frame.dtype == bool else 1
+            frame = ndi.zoom(frame,
+                             zoom_factors+[1.0],
+                             mode="nearest",
+                             grid_mode=False,
+                             order=order)
+            if smooth > 0:
+                frame = frame.astype(self.dtype)
             data_frames += (frame,)
 
         data = np.stack(data_frames)
 
-        if self.kind in ['scalar']:
+        # if self.kind in ['scalar']:
-            data = data.astype(dtype)
+        #     data = data.astype(dtype)
 
         # TXYZ > TXYZC
-        if self.kind in ['label', 'scalar']:
+        # if self.kind in ['label', 'scalar']:
-            data = np.expand_dims(data, axis=-1)  # expend channel
+        #     data = np.expand_dims(data, axis=-1)  # expend channel
 
         self.data = data
+
+        mat_scale = transforms3d.zooms.zfdir2aff(factors[0])
+        self.affine = np.dot(self.affine, mat_scale)

bioxelnodes/bioxel/parse.py

@@ -1,6 +1,5 @@
 from pathlib import Path
 import numpy as np
-from .layer import Layer
 
 # 3rd-party
 import SimpleITK as sitk
@@ -42,7 +41,8 @@ DICOM_EXTS = ['', '.dcm', '.DCM', '.DICOM', '.ima', '.IMA']
 SEQUENCE_EXTS = ['.bmp', '.BMP',
                  '.jpg', '.JPG', '.jpeg', '.JPEG',
                  '.tif', '.TIF', '.tiff', '.TIFF',
-                 '.png', '.PNG']
+                 '.png', '.PNG',
+                 '.mrc']
 
 
 def get_ext(filepath: Path) -> str:
@@ -61,21 +61,44 @@ def get_ext(filepath: Path) -> str:
     elif filepath.name.endswith(".map.gz"):
         return ".map.gz"
     else:
-        return filepath.suffix
+        suffix = filepath.suffix
+        return "" if len(suffix) > 5 else suffix
 
 
-def get_file_name(filepath: Path):
+def get_filename(filepath: Path):
     ext = get_ext(filepath)
-    return filepath.name.removesuffix(ext).replace(" ", "-")
+    return filepath.name.removesuffix(ext)
 
 
-def get_file_number(filepath: Path) -> str:
+def get_filename_parts(filepath: Path) -> str:
-    name = get_file_name(filepath)
+    def has_digits(s):
+        return any(char.isdigit() for char in s)
+
+    name = get_filename(filepath)
+    parts = name.replace(".", " ").replace("_", " ").split(" ")
+    skip_prefixs = ["CH", "ch", "channel"]
+    number_part = None
+    number_part_i = None
+
+    for i, part in enumerate(parts[::-1]):
+        if has_digits(part):
+            if not any([part.startswith(prefix) for prefix in skip_prefixs]):
+                number_part = part
+                number_part_i = len(parts)-i
+                break
+
+    if number_part is None:
+        return name, "", ""
+
+    prefix_parts = parts[:number_part_i-1]
+    prefix_parts_count = sum([len(part)+1 for part in prefix_parts])
+
     digits = ""
+    suffix = ""
 
     # Iterate through the characters in reverse order
     started = False
-    for char in name[::-1]:
+    for char in number_part[::-1]:
         if char.isdigit():
             started = True
             # If the character is a digit, add it to the digits string
@@ -84,20 +107,33 @@ def get_file_number(filepath: Path) -> str:
             if started:
                 # If a non-digit character is encountered, stop the loop
                 break
+            else:
+                suffix += char
+
+    digits = digits[::-1]
+
+    prefix_parts_count += len(number_part) - \
+        len(digits) - len(suffix)
 
     # Reverse the digits string to get the correct order
-    return digits[::-1]
+    prefix = name[:prefix_parts_count]
+    suffix = name[prefix_parts_count+len(digits):]
+
+    return prefix, digits, suffix
 
 
-def get_sequence_name(filepath: Path) -> str:
+def get_file_no_digits_name(filepath: Path) -> str:
-    name = get_file_name(filepath)
+    prefix, digits, suffix = get_filename_parts(filepath)
-    number = get_file_number(filepath)
+    prefix = remove_end_str(prefix, "_")
-    return name.removesuffix(number)
+    prefix = remove_end_str(prefix, ".")
+    prefix = remove_end_str(prefix, "-")
+    prefix = remove_end_str(prefix, " ")
+    return prefix + suffix
 
 
-def get_sequence_index(filepath: Path) -> int:
+def get_file_index(filepath: Path) -> int:
-    number = get_file_number(filepath)
+    prefix, digits, suffix = get_filename_parts(filepath)
-    return int(number) if number != "" else 0
+    return int(digits) if digits != "" else 0
 
 
 def collect_sequence(filepath: Path):
@@ -105,8 +141,8 @@ def collect_sequence(filepath: Path):
     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):
+                and get_file_no_digits_name(filepath) == get_file_no_digits_name(f):
-            index = get_sequence_index(f)
+            index = get_file_index(f)
             file_dict[index] = f
 
     # reomve isolated seq file
@@ -124,7 +160,13 @@ def collect_sequence(filepath: Path):
     return sequence
 
 
-def parse_volumetric_data(data_file: str, series_id="", progress_callback=None) -> Layer:
+def remove_end_str(string: str, end: str):
+    while string.endswith(end) and len(string) > 0:
+        string = string.removesuffix(end)
+    return string
+
+
+def parse_volumetric_data(data_file: str, series_id="", progress_callback=None):
     """Parse any volumetric data to numpy with shap (T,X,Y,Z,C)
 
     Args:
@@ -139,7 +181,7 @@ def parse_volumetric_data(data_file: str, series_id="", progress_callback=None)
     ext = get_ext(data_path)
 
     if progress_callback:
-        progress_callback(0, "Reading the Data...")
+        progress_callback(0.0, "Reading the Data...")
 
     is_sequence = False
     if ext in SEQUENCE_EXTS:
@@ -181,7 +223,7 @@ def parse_volumetric_data(data_file: str, series_id="", progress_callback=None)
             elif mrc.is_volume_stack():
                 data = np.expand_dims(data, axis=-1)  # expend channel
 
-            name = get_file_name(data_path)
+            name = get_file_no_digits_name(data_path)
             spacing = (mrc.voxel_size.x,
                        mrc.voxel_size.y,
                        mrc.voxel_size.z)
@@ -245,7 +287,7 @@ def parse_volumetric_data(data_file: str, series_id="", progress_callback=None)
             except:
                 ...
 
-            name = get_file_name(data_path)
+            name = get_file_no_digits_name(data_path)
         except:
             ...
 
@@ -269,6 +311,7 @@ def parse_volumetric_data(data_file: str, series_id="", progress_callback=None)
             def get_meta(key):
                 try:
                     stirng = reader.GetMetaData(0, key).removesuffix(" ")
+                    stirng.encode('utf-8')
                     if stirng in ["No study description",
                                   "No series description",
                                   ""]:
@@ -297,10 +340,10 @@ def parse_volumetric_data(data_file: str, series_id="", progress_callback=None)
 
         elif ext in SEQUENCE_EXTS and is_sequence:
             itk_image = sitk.ReadImage(sequence)
-            name = get_sequence_name(data_path)
+            name = get_file_no_digits_name(data_path)
         else:
             itk_image = sitk.ReadImage(data_path)
-            name = get_file_name(data_path)
+            name = get_filename(data_path)
 
         # for key in itk_image.GetMetaDataKeys():
         #     print(f"{key},{itk_image.GetMetaData(key)}")

bioxelnodes/bioxelutils/common.py

@@ -0,0 +1,270 @@
+from ast import literal_eval
+from pathlib import Path
+import bpy
+
+from ..constants import LATEST_NODE_LIB_PATH, NODE_LIB_DIRPATH, VERSIONS
+from ..utils import get_cache_dir
+
+
+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 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 get_layer_prop_value(layer_obj: bpy.types.Object, prop_name: str):
+    node_group = layer_obj.modifiers[0].node_group
+    layer_node = get_nodes_by_type(node_group, "BioxelNodes__Layer")[0]
+    prop = layer_node.inputs.get(prop_name)
+    if prop is None:
+        return None
+
+    value = prop.default_value
+
+    if type(value).__name__ == "bpy_prop_array":
+        value = tuple(value)
+        return tuple([int(v) for v in value]) \
+            if prop in ["shape"] else value
+    elif type(value).__name__ == "str":
+        return str(value)
+    elif type(value).__name__ == "float":
+        value = float(value)
+        return round(value, 2) \
+            if prop in ["bioxel_size"] else value
+    elif type(value).__name__ == "int":
+        value = int(value)
+        return value
+    else:
+        return value
+
+
+def get_layer_name(layer_obj):
+    return get_layer_prop_value(layer_obj, "name")
+
+
+def get_layer_kind(layer_obj):
+    return get_layer_prop_value(layer_obj, "kind")
+
+
+def get_layer_label(layer_obj):
+    name = get_layer_name(layer_obj)
+    # kind = get_layer_kind(layer_obj)
+
+    label = f"{name}"
+
+    if is_missing_layer(layer_obj):
+        return "**MISSING**" + label
+    elif is_temp_layer(layer_obj):
+        return "* " + label
+    else:
+        return label
+
+
+def is_missing_layer(layer_obj):
+    cache_filepath = Path(bpy.path.abspath(
+        layer_obj.data.filepath)).resolve()
+    return not cache_filepath.is_file()
+
+
+def is_temp_layer(layer_obj):
+    cache_filepath = Path(bpy.path.abspath(
+        layer_obj.data.filepath)).resolve()
+    cache_dirpath = Path(get_cache_dir())
+    return cache_dirpath in cache_filepath.parents
+
+
+def set_layer_prop_value(layer_obj: bpy.types.Object, prop: str, value):
+    node_group = layer_obj.modifiers[0].node_group
+    layer_node = get_nodes_by_type(node_group, "BioxelNodes__Layer")[0]
+    layer_node.inputs[prop].default_value = value
+
+
+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.data.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.data.objects:
+        if get_layer_obj(obj):
+            layer_objs.append(obj)
+
+    return layer_objs
+
+
+def add_driver(target, target_prop, var_sources, expression):
+    driver = target.driver_add(target_prop)
+    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):
+    drivers = [
+        {
+            "source": source,
+            "prop": source_prop
+        }
+    ]
+    expression = "var0"
+    add_driver(target, target_prop, drivers, expression)
+
+
+def read_file_prop(content: str):
+    props = {}
+    for line in content.split("\n"):
+        line = line.replace(" ", "")
+        p = line.split("=")[0]
+        if p != "":
+            v = line.split("=")[-1]
+            props[p] = v
+    return props
+
+
+def write_file_prop(props: dict):
+    lines = []
+    for p, v in props.items():
+        lines.append(f"{p} = {v}")
+    return "\n".join(lines)
+
+
+def set_file_prop(prop, value):
+    if bpy.data.texts.get("BioxelNodes") is None:
+        bpy.data.texts.new("BioxelNodes")
+
+    props = read_file_prop(bpy.data.texts["BioxelNodes"].as_string())
+    props[prop] = value
+    bpy.data.texts["BioxelNodes"].clear()
+    bpy.data.texts["BioxelNodes"].write(write_file_prop(props))
+
+
+def get_file_prop(prop):
+    if bpy.data.texts.get("BioxelNodes") is None:
+        bpy.data.texts.new("BioxelNodes")
+
+    props = read_file_prop(bpy.data.texts["BioxelNodes"].as_string())
+    return props.get(prop)
+
+
+def get_node_version():
+    node_version = get_file_prop("node_version")
+    return literal_eval(node_version) if node_version else None
+
+
+def is_incompatible():
+    node_version = get_node_version()
+    if node_version is None:
+        for node_group in bpy.data.node_groups:
+            if node_group.name.startswith("BioxelNodes"):
+                return True
+    else:
+        addon_version = VERSIONS[0]["node_version"]
+        if node_version[0] != addon_version[0]\
+                or node_version[1] != addon_version[1]:
+            return True
+
+    return False
+
+
+def get_node_lib_path(node_version):
+    version_str = "v"+".".join([str(i) for i in list(node_version)])
+    lib_filename = f"BioxelNodes_{version_str}.blend"
+    return Path(NODE_LIB_DIRPATH,
+                lib_filename).resolve()
+
+
+def local_lib_not_updated():
+    addon_version = VERSIONS[0]["node_version"]
+    addon_lib_path = LATEST_NODE_LIB_PATH
+
+    use_local = False
+    for node_group in bpy.data.node_groups:
+        if node_group.name.startswith("BioxelNodes"):
+            lib = node_group.library
+            if lib:
+                lib_path = Path(bpy.path.abspath(lib.filepath)).resolve()
+                if lib_path != addon_lib_path:
+                    use_local = True
+                    break
+
+    not_update = get_node_version() != addon_version
+    return use_local and not_update
+
+
+def get_output_node(node_group):
+    try:
+        output_node = get_nodes_by_type(node_group,
+                                        'NodeGroupOutput')[0]
+    except:
+        output_node = node_group.nodes.new("NodeGroupOutput")
+
+    return output_node

bioxelnodes/bioxelutils/container.py

@@ -5,10 +5,13 @@ 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 .layer import Layer, layer_to_obj, obj_to_layer
-from ..nodes import custom_nodes
+from .common import (get_container_layer_objs,
-from .node import get_nodes_by_type, move_node_to_node
+                     get_layer_prop_value,
-
+                     get_nodes_by_type, get_output_node,
+                     move_node_to_node)
+from .node import add_node_to_graph
+from ..utils import get_use_link
 
 NODE_TYPE = {
     "label": "BioxelNodes_MaskByLabel",
@@ -66,51 +69,6 @@ def calc_bbox_verts(origin: tuple, size: tuple):
     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]
@@ -119,8 +77,34 @@ def obj_to_container(container_obj: bpy.types.Object):
     return container
 
 
+def add_layers(layers: list[Layer],
+               container_obj: bpy.types.Object,
+               cache_dir: str):
+
+    node_group = container_obj.modifiers[0].node_group
+    output_node = get_output_node(node_group)
+
+    for i, layer in enumerate(layers):
+        layer_obj = layer_to_obj(layer, container_obj, cache_dir)
+        fetch_node = add_node_to_graph("FetchLayer",
+                                       node_group,
+                                       use_link=get_use_link())
+        fetch_node.label = get_layer_prop_value(layer_obj, "name")
+        fetch_node.inputs[0].default_value = layer_obj
+
+        if len(output_node.inputs[0].links) == 0:
+            node_group.links.new(fetch_node.outputs[0],
+                                 output_node.inputs[0])
+            move_node_to_node(fetch_node, output_node, (-600, 0))
+        else:
+            move_node_to_node(fetch_node, output_node, (0, -100 * (i+1)))
+
+    return container_obj
+
+
 def container_to_obj(container: Container,
                      scene_scale: float,
+                     step_size: float,
                      cache_dir: str):
     # Wrapper a Container
 
@@ -151,30 +135,33 @@ def container_to_obj(container: Container,
     container_obj.name = container.name
     container_obj.data.name = container.name
     container_obj.show_in_front = True
+
+    container_obj.lock_location[0] = True
+    container_obj.lock_location[1] = True
+    container_obj.lock_location[2] = True
+
+    container_obj.lock_rotation[0] = True
+    container_obj.lock_rotation[1] = True
+    container_obj.lock_rotation[2] = True
+
+    container_obj.lock_scale[0] = True
+    container_obj.lock_scale[1] = True
+    container_obj.lock_scale[2] = True
+
     container_obj['bioxel_container'] = True
+    container_obj["scene_scale"] = scene_scale
+    container_obj["step_size"] = step_size
 
-    bpy.ops.node.new_geometry_nodes_modifier()
+    modifier = container_obj.modifiers.new("GeometryNodes", 'NODES')
-    container_node_group = container_obj.modifiers[0].node_group
+    node_group = bpy.data.node_groups.new('GeometryNodes', 'GeometryNodeTree')
-    input_node = get_nodes_by_type(container_node_group,
+    node_group.interface.new_socket(name="Output",
-                                   'NodeGroupInput')[0]
+                                    in_out="OUTPUT",
-    container_node_group.links.remove(
+                                    socket_type="NodeSocketGeometry")
-        input_node.outputs[0].links[0])
+    modifier.node_group = node_group
+    node_group.nodes.new("NodeGroupOutput")
 
-    for i, layer in enumerate(container.layers):
+    container_obj = add_layers(container.layers,
-        layer_obj = layer_to_obj(layer, container_obj, cache_dir)
+                               container_obj=container_obj,
-        mask_node = custom_nodes.add_node(container_node_group,
+                               cache_dir=cache_dir)
-                                          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

@@ -7,35 +7,11 @@ 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
+from ..utils import get_use_link
-
+from .node import add_node_to_graph
-
+from .common import (get_layer_prop_value,
-def get_layer_obj(current_obj: bpy.types.Object):
+                     move_node_between_nodes)
-    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):
@@ -51,7 +27,11 @@ def obj_to_layer(layer_obj: bpy.types.Object):
             grids, base_metadata = vdb.readAll(str(f))
             grid = grids[0]
             metadata = grid.metadata
-            data_frame = np.ndarray(grid["data_shape"], np.float32)
+            if grid["layer_kind"] in ['label', 'scalar']:
+                data_shape = grid["data_shape"]
+            else:
+                data_shape = tuple(list(grid["data_shape"]) + [3])
+            data_frame = np.ndarray(data_shape, np.float32)
             grid.copyToArray(data_frame)
             data_frames += (data_frame,)
         data = np.stack(data_frames)
@@ -59,15 +39,24 @@ def obj_to_layer(layer_obj: bpy.types.Object):
         grids, base_metadata = vdb.readAll(str(cache_filepath))
         grid = grids[0]
         metadata = grid.metadata
-        data = np.ndarray(grid["data_shape"], np.float32)
+        if grid["layer_kind"] in ['label', 'scalar']:
+            data_shape = grid["data_shape"]
+        else:
+            data_shape = tuple(list(grid["data_shape"]) + [3])
+        data = np.ndarray(data_shape, np.float32)
         grid.copyToArray(data)
         data = np.expand_dims(data, axis=0)  # expend frame
 
-    name = metadata["layer_name"]
+    name = get_layer_prop_value(layer_obj, "name") \
-    kind = metadata["layer_kind"]
+        or metadata["layer_name"]
+    kind = get_layer_prop_value(layer_obj, "kind") \
+        or metadata["layer_kind"]
     affine = metadata["layer_affine"]
-    dtype = metadata.get("data_dtype") or "float32"
+    dtype = get_layer_prop_value(layer_obj, "dtype") \
-    offset = metadata.get("data_offset") or 0
+        or metadata.get("data_dtype") or "float32"
+    offset = get_layer_prop_value(layer_obj, "offset") \
+        or metadata.get("data_offset") or 0
+
     data = data - np.full_like(data, offset)
     data = data.astype(dtype)
 
@@ -110,6 +99,7 @@ def layer_to_obj(layer: Layer,
         "data_offset": offset
     }
 
+    layer_display_name = f"{container_obj.name}_{layer.name}"
     if layer.frame_count > 1:
         print(f"Saving the Cache of {layer.name}...")
         vdb_name = str(uuid4())
@@ -118,8 +108,14 @@ def layer_to_obj(layer: Layer,
 
         cache_filepaths = []
         for f in range(layer.frame_count):
+            if layer.kind in ['label', 'scalar']:
                 grid = vdb.FloatGrid()
                 grid.copyFromArray(data[f, :, :, :].copy().astype(np.float32))
+            else:
+                # color
+                grid = vdb.Vec3SGrid()
+                grid.copyFromArray(
+                    data[f, :, :, :, :].copy().astype(np.float32))
             grid.transform = vdb.createLinearTransform(
                 layer.affine.transpose())
             grid.metadata = metadata
@@ -130,17 +126,14 @@ def layer_to_obj(layer: Layer,
             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:
+        if layer.kind in ['label', 'scalar']:
             grid = vdb.FloatGrid()
             grid.copyFromArray(data[0, :, :, :].copy().astype(np.float32))
+        else:
+            # color
+            grid = vdb.Vec3SGrid()
+            grid.copyFromArray(data[0, :, :, :, :].copy().astype(np.float32))
         grid.transform = vdb.createLinearTransform(
             layer.affine.transpose())
         grid.metadata = metadata
@@ -151,52 +144,37 @@ def layer_to_obj(layer: Layer,
         vdb.write(str(cache_filepath), grids=[grid])
         cache_filepaths = [cache_filepath]
 
-        print(f"Loading the Cache of {layer.name}...")
+    layer_data = bpy.data.volumes.new(layer_display_name)
-        bpy.ops.object.volume_import(filepath=str(cache_filepaths[0]),
+    layer_data.render.space = 'WORLD'
-                                     align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
+    scene_scale = container_obj.get("scene_scale") or 0.01
+    step_size = container_obj.get("step_size") or 1
+    layer_data.render.step_size = scene_scale * step_size
+    layer_data.sequence_mode = 'REPEAT'
+    layer_data.filepath = str(cache_filepaths[0])
 
-    layer_obj = bpy.context.active_object
+    if layer.frame_count > 1:
-    layer_obj.data.sequence_mode = 'REPEAT'
+        layer_data.is_sequence = True
-
+        layer_data.frame_duration = layer.frame_count
-    # Set props to VDB object
+    else:
-    layer_obj.name = f"{container_obj.name}_{layer.name}"
+        layer_data.is_sequence = False
-    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 = bpy.data.objects.new(layer_display_name, layer_data)
     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()
+    modifier = layer_obj.modifiers.new("GeometryNodes", 'NODES')
-    node_group = layer_obj.modifiers[0].node_group
+    node_group = bpy.data.node_groups.new('GeometryNodes', 'GeometryNodeTree')
-    layer_node = custom_nodes.add_node(node_group,
+    node_group.interface.new_socket(name="Cache",
-                                          "BioxelNodes__Layer")
+                                    in_out="INPUT",
+                                    socket_type="NodeSocketGeometry")
+    node_group.interface.new_socket(name="Layer",
+                                    in_out="OUTPUT",
+                                    socket_type="NodeSocketGeometry")
+    modifier.node_group = node_group
+
+    layer_node = add_node_to_graph("_Layer",
+                                   node_group,
+                                   use_link=get_use_link())
 
     layer_node.inputs['name'].default_value = layer.name
     layer_node.inputs['shape'].default_value = layer.shape
@@ -207,19 +185,18 @@ def layer_to_obj(layer: Layer,
             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,
+    layer_node.inputs['unique'].default_value = random.uniform(0, 1)
-                                                              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['frame_count'].default_value = layer.frame_count
+    layer_node.inputs['channel_count'].default_value = layer.channel_count
     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,
+    input_node = node_group.nodes.new("NodeGroupInput")
-                                   'NodeGroupInput')[0]
+    output_node = node_group.nodes.new("NodeGroupOutput")
-    output_node = get_nodes_by_type(node_group,
-                                    'NodeGroupOutput')[0]
 
     node_group.links.new(input_node.outputs[0],
                          layer_node.inputs[0])
@@ -229,4 +206,6 @@ def layer_to_obj(layer: Layer,
     move_node_between_nodes(
         layer_node, [input_node, output_node])
 
+    layer_obj.parent = container_obj
+
     return layer_obj

bioxelnodes/bioxelutils/node.py

@@ -1,26 +1,71 @@
-def move_node_to_node(node, target_node, offset=(0, 0)):
+from pathlib import Path
-    node.location.x = target_node.location.x + offset[0]
+import bpy
-    node.location.y = target_node.location.y + offset[1]
+
+from .common import get_file_prop, set_file_prop
+from ..exceptions import NoFound
+
+from ..constants import LATEST_NODE_LIB_PATH, VERSIONS
 
 
-def move_node_between_nodes(node, target_nodes, offset=(0, 0)):
+def get_node_tree(node_type: str, use_link=True):
-    xs = []
+    # unannotate below for local debug in node lib file.
-    ys = []
+    # node_group = bpy.data.node_groups[node_type]
-    for target_node in target_nodes:
+    # return node_group
-        xs.append(target_node.location.x)
-        ys.append(target_node.location.y)
 
-    node.location.x = sum(xs) / len(xs) + offset[0]
+    # added node is always from latest node version
-    node.location.y = sum(ys) / len(ys) + offset[1]
+    addon_version = VERSIONS[0]["node_version"]
+    addon_lib_path = LATEST_NODE_LIB_PATH
+
+    if get_file_prop("node_version") is None:
+        set_file_prop("node_version", addon_version)
+
+    local_lib = None
+    for node_group in bpy.data.node_groups:
+        if node_group.name.startswith("BioxelNodes"):
+            lib = node_group.library
+            if lib:
+                lib_path = Path(bpy.path.abspath(lib.filepath)).resolve()
+                if lib_path != addon_lib_path:
+                    local_lib = lib.filepath
+                    break
+
+    # local lib first
+    lib_path_str = local_lib or str(addon_lib_path)
+
+    with bpy.data.libraries.load(lib_path_str,
+                                 link=use_link,
+                                 relative=True) as (data_from, data_to):
+        data_to.node_groups = [n for n in data_from.node_groups
+                               if n == node_type]
+
+    node_tree = data_to.node_groups[0]
+
+    if node_tree is None:
+        raise NoFound('No custom node found')
+
+    return node_tree
 
 
-def get_node_type(node):
+def assign_node_tree(node, node_tree):
-    node_type = type(node).__name__
+    node.node_tree = node_tree
-    if node_type == "GeometryNodeGroup":
+    node.width = 200.0
-        node_type = node.node_tree.name
+    node.name = node_tree.name
-
+    return node
-    return node_type
 
 
-def get_nodes_by_type(node_group, type_name: str):
+def add_node_to_graph(node_name: str, node_group, node_label=None, use_link=True):
-    return [node for node in node_group.nodes if get_node_type(node) == type_name]
+    node_type = f"BioxelNodes_{node_name}"
+    node_label = node_label or node_name
+
+    # Deselect all nodes first
+    for node in node_group.nodes:
+        if node.select:
+            node.select = False
+
+    node_tree = get_node_tree(node_type, use_link)
+    node = node_group.nodes.new("GeometryNodeGroup")
+    assign_node_tree(node, node_tree)
+
+    node.label = node_label
+    node.show_options = False
+    return node

bioxelnodes/blender_manifest.toml

@@ -1,7 +1,7 @@
 schema_version = "1.0.0"
 
 id = "bioxelnodes"
-version = "0.3.2"
+version = "1.0.5"
 name = "Bioxel Nodes"
 tagline = "For scientific volumetric data visualization in Blender"
 maintainer = "Ma Nan <icrdr2010@outlook.com>"
@@ -10,7 +10,7 @@ website = "https://omoolab.github.io/BioxelNodes/latest"
 
 tags = ["Geometry Nodes", "Render", "Import-Export"]
 blender_version_min = "4.2.0"
-license = ["SPDX:MIT"]
+license = ['SPDX:GPL-3.0-or-later']
 copyright = ["2024 OmooLab"]
 platforms = ["windows-x64", "linux-x64", "macos-arm64", "macos-x64"]
 
@@ -19,10 +19,10 @@ wheels = [
   "./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-5.3.0-cp311-cp311-win_amd64.whl",
-  "./wheels/lxml-5.2.2-cp311-cp311-macosx_10_9_arm64.whl",
+  "./wheels/lxml-5.3.0-cp311-cp311-macosx_10_9_arm64.whl",
-  "./wheels/lxml-5.2.2-cp311-cp311-macosx_10_9_x86_64.whl",
+  "./wheels/lxml-5.3.0-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/lxml-5.3.0-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",
@@ -30,9 +30,8 @@ wheels = [
   "./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",
+  "./wheels/transforms3d-0.4.2-py3-none-any.whl"
 ]
 
 [permissions]
 files = "Import/export volume data from/to disk"
-

bioxelnodes/constants.py

@@ -0,0 +1,251 @@
+from pathlib import Path
+
+VERSIONS = [{"label": "Latest", "node_version": (1, 0, 5)},
+            {"label": "v0.3.x", "node_version": (0, 3, 3)},
+            {"label": "v0.2.x", "node_version": (0, 2, 9)}]
+
+NODE_LIB_DIRPATH = Path(Path(__file__).parent,
+                        "assets/Nodes").resolve()
+
+LATEST_NODE_LIB_PATH = lib_path = Path(NODE_LIB_DIRPATH,
+                                  "BioxelNodes_latest.blend").resolve()
+
+COMPONENT_OUTPUT_NODES = [
+    "CutoutByThreshold",
+    "CutoutByRange",
+    "CutoutByHue",
+    "JoinComponent",
+    "SetProperties",
+    "SetColor",
+    "SetColorByColor",
+    "SetColorByColor",
+    "SetColorByRamp2",
+    "SetColorByRamp3",
+    "SetColorByRamp4",
+    "SetColorByRamp5",
+    "Cut",
+]
+
+MENU_ITEMS = [
+    {
+        'label': 'Component',
+        'icon': 'OUTLINER_DATA_VOLUME',
+        'items': [
+            {
+                'label': 'Cutout by Threshold',
+                'icon': 'EMPTY_SINGLE_ARROW',
+                'name': 'CutoutByThreshold',
+                'description': ''
+            },
+            {
+                'label': 'Cutout by Range',
+                'icon': 'IPO_CONSTANT',
+                'name': 'CutoutByRange',
+                'description': ''
+            },
+            {
+                'label': 'Cutout by Hue',
+                'icon': 'COLOR',
+                'name': 'CutoutByHue',
+                'description': ''
+            },
+            "separator",
+            {
+                'label': 'To Surface',
+                'icon': 'MESH_DATA',
+                'name': 'ToSurface',
+                'description': ''
+            },
+            {
+                'label': 'Join Component',
+                'icon': 'CONSTRAINT_BONE',
+                'name': 'JoinComponent',
+                'description': ''
+            },
+            {
+                'label': 'Slice',
+                'icon': 'TEXTURE',
+                'name': 'Slice',
+                'description': ''
+            }
+        ]
+    },
+    {
+        'label': 'Property',
+        'icon': 'PROPERTIES',
+        'items': [
+            {
+                'label': 'Set Properties',
+                'icon': 'PROPERTIES',
+                'name': 'SetProperties',
+                'description': ''
+            },
+            "separator",
+            {
+                'label': 'Set Color',
+                'icon': 'IPO_SINE',
+                'name': 'SetColor',
+                'description': ''
+            },
+            {
+                'label': 'Set Color by Color',
+                'icon': 'IPO_QUINT',
+                'name': 'SetColorByColor',
+                'description': ''
+            },
+            {
+                'label': 'Set Color by Ramp 2',
+                'icon': 'IPO_QUAD',
+                'name': 'SetColorByRamp2',
+                'description': ''
+            },
+            {
+                'label': 'Set Color by Ramp 3',
+                'icon': 'IPO_CUBIC',
+                'name': 'SetColorByRamp3',
+                'description': ''
+            },
+            {
+                'label': 'Set Color by Ramp 4',
+                'icon': 'IPO_QUART',
+                'name': 'SetColorByRamp4',
+                'description': ''
+            },
+            {
+                'label': 'Set Color by Ramp 5',
+                'icon': 'IPO_QUINT',
+                'name': 'SetColorByRamp5',
+                'description': ''
+            }
+        ]
+    },
+    {
+        'label': 'Surface',
+        'icon': 'MESH_DATA',
+        'items': [
+            {
+                'label': 'Membrane Shader',
+                'icon': 'NODE_MATERIAL',
+                'name': 'AssignMembraneShader',
+                'description': ''
+            },
+            {
+                'label': 'Solid Shader',
+                'icon': 'SHADING_SOLID',
+                'name': 'AssignSolidShader',
+                'description': ''
+            },
+            {
+                'label': 'Slime Shader',
+                'icon': 'OUTLINER_DATA_META',
+                'name': 'AssignSlimeShader',
+                'description': ''
+            },
+
+        ]
+    },
+    {
+        'label': 'Transform',
+        'icon': 'EMPTY_AXIS',
+        'items': [
+            {
+                'label': 'Transform',
+                'icon': 'EMPTY_AXIS',
+                'name': 'Transform',
+                'description': ''
+            },
+            {
+                'label': 'Transform Parent',
+                'icon': 'ORIENTATION_PARENT',
+                'name': 'TransformParent',
+                'description': ''
+            },
+            {
+                'label': 'ReCenter',
+                'icon': 'PROP_CON',
+                'name': 'ReCenter',
+                'description': ''
+            },
+            {
+                'label': 'Extract Transform',
+                'icon': 'EMPTY_AXIS',
+                'name': 'ExtractTransform',
+                'description': ''
+            },
+        ]
+    },
+    {
+        'label': 'Cut',
+        'icon': 'MOD_BEVEL',
+        'items': [
+            {
+                'label': 'Cut',
+                'icon': 'MOD_BEVEL',
+                'name': 'Cut',
+                'description': ''
+            },
+            "separator",
+            {
+                'label': 'Primitive Cutter',
+                'icon': 'MOD_LINEART',
+                'name': 'PrimitiveCutter',
+                'description': ''
+            },
+            {
+                'label': 'Object Cutter',
+                'icon': 'MESH_PLANE',
+                'name': 'ObjectCutter',
+                'description': ''
+            }
+        ]
+    },
+    {
+        'label': 'Extra',
+        'icon': 'MODIFIER',
+        'items': [
+            {
+                'label': 'Fetch Mesh',
+                'icon': 'OUTLINER_OB_MESH',
+                'name': 'FetchMesh',
+                'description': ''
+            },
+            {
+                'label': 'Fetch Volume',
+                'icon': 'OUTLINER_OB_VOLUME',
+                'name': 'FetchVolume',
+                'description': ''
+            },
+            {
+                'label': 'Fetch Shape Wire',
+                'icon': 'FILE_VOLUME',
+                'name': 'FetchShapeWire',
+                'description': ''
+            },
+            {
+                'label': 'Fetch Bbox Wire',
+                'icon': 'MESH_CUBE',
+                'name': 'FetchBboxWire',
+                'description': ''
+            },
+            "separator",
+            {
+                'label': 'Inflate',
+                'icon': 'OUTLINER_OB_META',
+                'name': 'Inflate',
+                'description': ''
+            },
+            {
+                'label': 'Smooth',
+                'icon': 'MOD_SMOOTH',
+                'name': 'Smooth',
+                'description': ''
+            },
+            {
+                'label': 'Remove Small Island',
+                'icon': 'FORCE_LENNARDJONES',
+                'name': 'RemoveSmallIsland',
+                'description': ''
+            }
+        ]
+    }
+]

bioxelnodes/customnodes/__init__.py

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

bioxelnodes/customnodes/menus.py

@@ -1,147 +0,0 @@
-import bpy
-from pathlib import Path
-from .nodes import AddCustomNode
-
-
-class CustomNodes():
-    def __init__(
-        self,
-        menu_items,
-        nodes_file,
-        class_prefix="CUSTOMNODES_MT_NODES",
-        root_label='CustomNodes',
-        root_icon='NONE'
-    ) -> None:
-        if not Path(nodes_file).is_file():
-            raise FileNotFoundError(str(Path(nodes_file).resolve()))
-
-        self.menu_items = menu_items
-        self.nodes_file = str(Path(nodes_file).resolve())
-        self.class_prefix = class_prefix
-        self.root_label = root_label
-        self.root_icon = root_icon
-        self.class_prefix = class_prefix
-
-        menu_classes = []
-        self._create_menu_class(
-            items=menu_items,
-            label=root_label,
-            menu_classes=menu_classes
-        )
-        self.menu_classes = menu_classes
-
-        idname = f"{class_prefix}_{root_label.replace(' ', '').upper()}"
-
-        def add_node_menu(self, context):
-            if ('GeometryNodeTree' == bpy.context.area.spaces[0].tree_type):
-                layout = self.layout
-                layout.separator()
-                layout.menu(idname, icon=root_icon)
-
-        self.add_node_menu = add_node_menu
-
-    def _create_menu_class(self, menu_classes, items, label='CustomNodes', icon=0, idname_namespace=None):
-        nodes_file = self.nodes_file
-        idname_namespace = idname_namespace or self.class_prefix
-        idname = f"{idname_namespace}_{label.replace(' ', '').upper()}"
-
-        # create submenu class if item is menu.
-        for item in items:
-            item_items = item.get('items') if item != 'separator' else None
-            if item_items:
-                menu_class = self._create_menu_class(
-                    menu_classes=menu_classes,
-                    items=item_items,
-                    label=item.get('label') or 'CustomNodes',
-                    icon=item.get('icon') or 0,
-                    idname_namespace=idname
-                )
-                item['menu_class'] = menu_class
-
-        # create menu class
-        class Menu(bpy.types.Menu):
-            bl_idname = idname
-            bl_label = label
-            nodes_file = self.nodes_file
-
-            def draw(self, context):
-                layout = self.layout
-
-                for item in items:
-                    # print(item)
-                    if item == "separator":
-                        layout.separator()
-                    elif item.get('menu_class'):
-                        layout.menu(
-                            item.get('menu_class').bl_idname,
-                            icon=item.get('icon') or 'NONE'
-                        )
-                    else:
-                        op = layout.operator(
-                            'customnodes.add_custom_node',
-                            text=item.get('label'),
-                            icon=item.get('icon') or 'NONE'
-                        )
-                        op.nodes_file = nodes_file
-                        op.node_type = item['node_type']
-                        op.node_label = item.get('label') or ""
-                        op.node_description = item.get(
-                            'node_description') or "Add Custom Node."
-                        op.node_link = item.get('link') or True
-                        op.node_callback = item.get('node_callback') or ""
-
-        menu_classes.append(Menu)
-        return Menu
-
-    def _find_item(self, found_items, menu_items, node_type: str):
-
-        for item in menu_items:
-            if item == 'separator':
-                continue
-
-            if item.get("node_type") == node_type:
-                found_items.append(item)
-
-            item_items = item.get('items')
-            if item_items:
-                self._find_item(found_items, item_items, node_type)
-
-    def find_item(self, node_type: str):
-        found_items = []
-        self._find_item(found_items, self.menu_items, node_type)
-        return found_items[0] if len(found_items) > 0 else None
-
-    def add_node(self, node_group, node_type: str):
-        item = self.find_item(node_type)
-        op = AddCustomNode()
-        op.nodes_file = self.nodes_file
-        op.node_type = node_type
-        if item:
-            op.node_label = item.get('label') or ""
-            op.node_link = item.get('link') or True
-            op.node_callback = item.get('node_callback') or ""
-        else:
-            op.node_label = ""
-            op.node_link = True
-            op.node_callback = ""
-        return op.add_node(node_group)
-
-    def register(self):
-        for cls in self.menu_classes:
-            bpy.utils.register_class(cls)
-
-        bpy.types.NODE_MT_add.append(self.add_node_menu)
-        bpy.types.Scene.customnodes_node_dir = bpy.props.StringProperty(
-            name="Node Directory",
-            subtype='DIR_PATH',
-            default="//"
-        )
-
-    def unregister(self):
-        bpy.types.NODE_MT_add.remove(self.add_node_menu)
-        try:
-            for cls in reversed(self.menu_classes):
-                bpy.utils.unregister_class(cls)
-
-        except RuntimeError:
-            pass

bioxelnodes/customnodes/nodes.py

@@ -1,127 +0,0 @@
-import bpy
-
-
-class AddCustomNode():
-
-    nodes_file: bpy.props.StringProperty(
-        name="nodes_file",
-        subtype='FILE_PATH',
-        default=""
-    )  # type: ignore
-
-    node_type: bpy.props.StringProperty(
-        name='node_type',
-        description='',
-        default='',
-        subtype='NONE',
-        maxlen=0
-    )  # type: ignore
-
-    node_label: bpy.props.StringProperty(
-        name='node_label',
-        default=''
-    )  # type: ignore
-
-    node_description: bpy.props.StringProperty(
-        name="node_description",
-        description="",
-        default="Add custom node group.",
-        subtype="NONE"
-    )  # type: ignore
-
-    node_link: bpy.props.BoolProperty(
-        name='node_link',
-        default=True
-    )  # type: ignore
-
-    node_callback: bpy.props.StringProperty(
-        name='node_callback',
-        default=''
-    )  # type: ignore
-
-    @classmethod
-    def description(cls, context, properties):
-        return properties.node_description
-
-    def assign_node_tree(self, node):
-        node.node_tree = bpy.data.node_groups[self.node_type]
-
-        node.width = 200.0
-        node.label = self.node_label or self.node_type
-        node.name = self.node_type
-
-        if self.node_callback:
-            exec(self.node_callback)
-
-        return node
-
-    def get_node_tree(self, node_type, node_link):
-        # try to get node from current file if exists
-        node_tree = bpy.data.node_groups.get(node_type)
-        # if not exists, get it from asset file.
-        if not node_tree:
-            bpy.ops.wm.append(
-                'EXEC_DEFAULT',
-                directory=f"{self.nodes_file}/NodeTree",
-                filename=node_type,
-                link=node_link,
-                use_recursive=True
-            )
-
-        node_tree = bpy.data.node_groups.get(node_type)
-        if node_tree:
-            # self.recursive_append_material(node_tree)
-            return node_tree
-        else:
-            raise RuntimeError('No custom node found')
-
-    def recursive_append_material(self, node_tree):
-        for child in node_tree.nodes:
-            material_socket = child.inputs.get('Material')
-            if material_socket:
-                print(material_socket.default_value)
-            try:
-                self.recursive_append_material(child.node_tree)
-            except:
-                ...
-
-    def add_node(self, node_group):
-        # Deselect all nodes first
-        for node in node_group.nodes:
-            if node.select:
-                node.select = False
-
-        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
-
-
-class CUSTOMNODES_OT_Add_Custom_Node(bpy.types.Operator, AddCustomNode):
-    bl_idname = "customnodes.add_custom_node"
-    bl_label = "Add Custom Node"
-    bl_options = {"REGISTER", "UNDO"}
-
-    def execute(self, context):
-        self.get_node_tree(self.node_type, self.node_link)
-
-        # intended to be called upon button press in the node tree
-        prev_context = bpy.context.area.type
-        bpy.context.area.type = 'NODE_EDITOR'
-        # actually invoke the operator to add a node to the current node tree
-        # use_transform=True ensures it appears where the user's mouse is and is currently
-        # being moved so the user can place it where they wish
-        bpy.ops.node.add_node(
-            'INVOKE_DEFAULT',
-            type='GeometryNodeGroup',
-            use_transform=True
-        )
-        bpy.context.area.type = prev_context
-        node = bpy.context.active_node
-
-        self.assign_node_tree(node)
-        node.show_options = False
-
-        return {"FINISHED"}

bioxelnodes/exceptions.py

@@ -2,3 +2,21 @@ class CancelledByUser(Exception):
     def __init__(self):
         message = 'Cancelled by user'
         super().__init__(message)
+
+
+class NoContent(Exception):
+    def __init__(self, message):
+        super().__init__(message)
+        self.message = message
+
+
+class NoFound(Exception):
+    def __init__(self, message):
+        super().__init__(message)
+        self.message = message
+
+
+class Incompatible(Exception):
+    def __init__(self, message):
+        super().__init__(message)
+        self.message = message

bioxelnodes/menus.py

@@ -1,156 +1,192 @@
 import bpy
 
-from .bioxelutils.container import get_container_objs_from_selection
+from .constants import MENU_ITEMS, VERSIONS
-from .operators.layer import (CombineLabels, SignScalar,
+from .node_menu import NodeMenu
+
+from .bioxelutils.common import (get_container_obj,
+                                 get_container_layer_objs, get_layer_label,
+                                 get_layer_prop_value, get_node_version, is_incompatible)
+from .operators.layer import (FetchLayer, RelocateLayer, RetimeLayer, RenameLayer,
+                              RemoveSelectedLayers, SaveSelectedLayersCache,
+                              ResampleLayer, SignScalar, CombineLabels,
                               FillByLabel, FillByThreshold, FillByRange)
-from .operators.container import (SaveContainer, LoadContainer,
+from .operators.container import (AddLocator, AddSlicer, ContainerProps,
+                                  SaveContainerLayersCache, RemoveContainerMissingLayers,
+                                  SaveContainer, LoadContainer,
                                   AddPieCutter, AddPlaneCutter,
                                   AddCylinderCutter, AddCubeCutter, AddSphereCutter,
-                                  PickBboxWire, PickMesh, PickVolume)
+                                  ExtractBboxWire, ExtractMesh, ExtractShapeWire,
-from .operators.io import (ExportVolumetricData,
+                                  ExtractNodeMesh, ExtractNodeBboxWire, ExtractNodeShapeWire)
-                           ImportAsLabelLayer, ImportAsScalarLayer)
+
-from .operators.misc import (CleanAllCaches,
+from .operators.io import (ImportAsLabel, ImportAsScalar, ImportAsColor)
-                             ReLinkNodes, SaveCaches, SaveStagedData)
+from .operators.misc import (CleanTemp, Help,
+                             ReLinkNodeLib, RemoveAllMissingLayers,
+                             RenderSettingPreset, SaveAllLayersCache,
+                             SaveNodeLib, SliceViewer)
 
 
-def container_is_selected():
+class IncompatibleMenu(bpy.types.Menu):
-    container_objs = get_container_objs_from_selection()
+    bl_idname = "BIOXELNODES_MT_INCOMPATIBLE"
-    return len(container_objs) > 0
+    bl_label = "Bioxel Nodes"
+
+    def draw(self, context):
+        tip_text = "please downgrade addon version."
+        node_version = get_node_version()
+        if node_version:
+            version_str = "v"+".".join([str(i) for i in list(node_version)])
+            tip_text = f"please downgrade addon version to {version_str}."
+
+        layout = self.layout
+        layout.label(text="Incompatible node version detected.")
+        layout.separator()
+        layout.label(
+            text="If you still want to edit this file with bioxel nodes, ")
+        layout.label(text=tip_text)
+        layout.separator()
+        layout.label(text="If this file is archived, "
+                     "please relink node library, ")
+        layout.label(text="check if it still works, "
+                     "then save node library.")
+        layout.separator()
+        layout.menu(ReLinkNodeLibMenu.bl_idname)
+        layout.operator(SaveNodeLib.bl_idname)
+
+        layout.separator()
+        layout.menu(DangerZoneMenu.bl_idname)
+
+        layout.separator()
+        layout.menu(RenderSettingMenu.bl_idname)
+
+        layout.separator()
+        layout.operator(Help.bl_idname,
+                        icon=Help.bl_icon)
 
 
-class PickFromContainerMenu(bpy.types.Menu):
+class FetchLayerMenu(bpy.types.Menu):
+    bl_idname = "BIOXELNODES_MT_ADD_LAYER"
+    bl_label = "Fetch Layer"
+
+    def draw(self, context):
+        container_obj = get_container_obj(bpy.context.active_object)
+        layer_objs = get_container_layer_objs(container_obj)
+        layout = self.layout
+
+        for layer_obj in layer_objs:
+            op = layout.operator(FetchLayer.bl_idname,
+                                 text=get_layer_label(layer_obj))
+            op.layer_obj_name = layer_obj.name
+
+
+class ExtractFromContainerMenu(bpy.types.Menu):
     bl_idname = "BIOXELNODES_MT_PICK"
-    bl_label = "Pick from Container"
+    bl_label = "Extract from Container"
 
     def draw(self, context):
         layout = self.layout
-        layout.operator(PickMesh.bl_idname)
+        layout.operator(ExtractMesh.bl_idname)
-        layout.operator(PickVolume.bl_idname)
+        layout.operator(ExtractShapeWire.bl_idname)
-        layout.operator(PickBboxWire.bl_idname)
+        layout.operator(ExtractBboxWire.bl_idname)
-
-
-class ModifyLayerMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_MODIFY_LAYERS"
-    bl_label = "Modify Layer"
-
-    def draw(self, context):
-        layout = self.layout
-        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)
 
 
 class AddCutterMenu(bpy.types.Menu):
     bl_idname = "BIOXELNODES_MT_CUTTERS"
-    bl_label = "Add a Cutter to Container"
+    bl_label = "Add a Cutter"
 
     def draw(self, context):
         layout = self.layout
-        layout.operator(AddPlaneCutter.bl_idname, text="Plane Cutter")
+        layout.operator(AddPlaneCutter.bl_idname,
-        layout.operator(AddCylinderCutter.bl_idname, text="Cylinder Cutter")
+                        icon=AddPlaneCutter.bl_icon, text="Plane Cutter")
-        layout.operator(AddCubeCutter.bl_idname, text="Cube Cutter")
+        layout.operator(AddCylinderCutter.bl_idname,
-        layout.operator(AddSphereCutter.bl_idname, text="Sphere Cutter")
+                        icon=AddCylinderCutter.bl_icon, text="Cylinder Cutter")
-        layout.operator(AddPieCutter.bl_idname, text="Pie Cutter")
+        layout.operator(AddCubeCutter.bl_idname,
+                        icon=AddCubeCutter.bl_icon, text="Cube Cutter")
+        layout.operator(AddSphereCutter.bl_idname,
+                        icon=AddSphereCutter.bl_icon, text="Sphere Cutter")
+        layout.operator(AddPieCutter.bl_idname,
+                        icon=AddPieCutter.bl_icon, text="Pie Cutter")
 
 
 class ImportLayerMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_LAYERS"
+    bl_idname = "BIOXELNODES_MT_IMPORTLAYER"
-    bl_label = "Import Volumetric Data"
+    bl_label = "Import Volumetric Data (Init)"
+    bl_icon = "FILE_NEW"
 
     def draw(self, context):
         layout = self.layout
-        layout.operator(ImportAsScalarLayer.bl_idname, text="as Scalar")
+        layout.operator(ImportAsScalar.bl_idname,
-        layout.operator(ImportAsLabelLayer.bl_idname, text="as Label")
+                        text="as Scalar")
+        layout.operator(ImportAsLabel.bl_idname,
+                        text="as Label")
+        layout.operator(ImportAsColor.bl_idname,
+                        text="as Color")
 
 
-class BioxelNodesView3DMenu(bpy.types.Menu):
+class AddLayerMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_VIEW3D"
+    bl_idname = "BIOXELNODES_MT_ADDLAYER"
-    bl_label = "Bioxel Nodes"
+    bl_label = "Import Volumetric Data (Add)"
+    bl_icon = "FILE_NEW"
 
     def draw(self, context):
         layout = self.layout
-        is_selected = container_is_selected()
+        layout.operator(ImportAsScalar.bl_idname,
-        layout.operator(ImportAsScalarLayer.bl_idname,
+                        text="as Scalar")
-                        text=ImportAsScalarLayer.bl_label+" (Add to)"
+        layout.operator(ImportAsLabel.bl_idname,
-                        if is_selected else ImportAsScalarLayer.bl_label+" (Init)")
+                        text="as Label")
-        layout.operator(ImportAsLabelLayer.bl_idname,
+        layout.operator(ImportAsColor.bl_idname,
-                        text=ImportAsLabelLayer.bl_label+" (Add to)"
+                        text="as Color")
-                        if is_selected else ImportAsLabelLayer.bl_label+" (Init)")
-        layout.separator()
-        layout.operator(AddPlaneCutter.bl_idname)
-        layout.operator(AddCylinderCutter.bl_idname)
-        layout.operator(AddCubeCutter.bl_idname)
-        layout.operator(AddSphereCutter.bl_idname)
-        layout.operator(AddPieCutter.bl_idname)
-        layout.separator()
-        layout.operator(PickMesh.bl_idname)
-        layout.operator(PickVolume.bl_idname)
-        layout.operator(PickBboxWire.bl_idname)
-        layout.separator()
-        layout.operator(SaveCaches.bl_idname)
 
 
-class BioxelNodesOutlinerMenu(bpy.types.Menu):
+class ModifyLayerMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_OUTLINER"
+    bl_idname = "BIOXELNODES_MT_MODIFYLAYER"
-    bl_label = "Bioxel Nodes"
+    bl_label = "Modify Layer"
+    bl_icon = "FILE_NEW"
 
     def draw(self, context):
         layout = self.layout
-        is_selected = container_is_selected()
+        layout.operator(SignScalar.bl_idname,
-        layout.operator(ImportAsScalarLayer.bl_idname,
+                        icon=SignScalar.bl_icon)
-                        text=ImportAsScalarLayer.bl_label+" (Add to)"
+        layout.operator(FillByThreshold.bl_idname,
-                        if is_selected else ImportAsScalarLayer.bl_label+" (Init)")
+                        icon=FillByThreshold.bl_icon)
-        layout.operator(ImportAsLabelLayer.bl_idname,
+        layout.operator(FillByRange.bl_idname,
-                        text=ImportAsLabelLayer.bl_label+" (Add to)"
+                        icon=FillByRange.bl_icon)
-                        if is_selected else ImportAsLabelLayer.bl_label+" (Init)")
+        layout.operator(FillByLabel.bl_idname,
-        layout.separator()
+                        icon=FillByLabel.bl_icon)
-        layout.operator(AddPlaneCutter.bl_idname)
+        layout.operator(CombineLabels.bl_idname,
-        layout.operator(AddCylinderCutter.bl_idname)
+                        icon=CombineLabels.bl_icon)
-        layout.operator(AddCubeCutter.bl_idname)
-        layout.operator(AddSphereCutter.bl_idname)
-        layout.operator(AddPieCutter.bl_idname)
-        layout.separator()
-        layout.operator(PickMesh.bl_idname)
-        layout.operator(PickVolume.bl_idname)
-        layout.operator(PickBboxWire.bl_idname)
-        layout.separator()
-        layout.operator(SaveCaches.bl_idname)
-        layout.separator()
-        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)
 
 
-def TOPBAR_FILE_IMPORT(self, context):
+class ReLinkNodeLibMenu(bpy.types.Menu):
+    bl_idname = "BIOXELNODES_MT_RELINK"
+    bl_label = "Relink Node Library"
+
+    def draw(self, context):
         layout = self.layout
-    is_selected = container_is_selected()
 
-    layout.separator()
+        for index, version in enumerate(VERSIONS):
-    layout.menu(ImportLayerMenu.bl_idname, text="Volumetric Data as Bioxel (Add to)"
+            op = layout.operator(ReLinkNodeLib.bl_idname,
-                if is_selected else "Volumetric Data as Bioxel (Init)")
+                                 text=version["label"])
+            op.index = index
 
 
-def TOPBAR_FILE_EXPORT(self, context):
+class RenderSettingMenu(bpy.types.Menu):
+    bl_idname = "BIOXELNODES_MT_RENDER"
+    bl_label = "Render Setting Presets"
+
+    def draw(self, context):
         layout = self.layout
-    layout.separator()
+        for k, v in RenderSettingPreset.PRESETS.items():
-    layout.operator(ExportVolumetricData.bl_idname,
+            op = layout.operator(RenderSettingPreset.bl_idname,
-                    text="Bioxel Layer (.vdb)")
+                                 text=v)
+            op.preset = k
 
 
-def VIEW3D_OBJECT(self, context):
+class DangerZoneMenu(bpy.types.Menu):
+    bl_idname = "BIOXELNODES_MT_DANGER"
+    bl_label = "Danger Zone"
+
+    def draw(self, context):
         layout = self.layout
-    layout.separator()
+        layout.operator(CleanTemp.bl_idname)
-    layout.menu(BioxelNodesView3DMenu.bl_idname, icon="FILE_VOLUME")
-
-
-def OUTLINER_OBJECT(self, context):
-    layout = self.layout
-    layout.separator()
-    layout.menu(BioxelNodesOutlinerMenu.bl_idname, icon="FILE_VOLUME")
 
 
 class BioxelNodesTopbarMenu(bpy.types.Menu):
@@ -159,39 +195,240 @@ class BioxelNodesTopbarMenu(bpy.types.Menu):
 
     def draw(self, context):
         layout = self.layout
-        is_selected = container_is_selected()
 
-        layout.menu(ImportLayerMenu.bl_idname, text=ImportLayerMenu.bl_label+" (Add to)"
+        layout.menu(ImportLayerMenu.bl_idname,
-                    if is_selected else ImportLayerMenu.bl_label+" (Init)")
+                    icon=ImportLayerMenu.bl_icon)
-        layout.separator()
         layout.operator(LoadContainer.bl_idname)
-        layout.operator(SaveContainer.bl_idname)
+
         layout.separator()
-        layout.menu(AddCutterMenu.bl_idname)
+        layout.operator(SaveAllLayersCache.bl_idname)
-        layout.menu(PickFromContainerMenu.bl_idname)
+        layout.operator(RemoveAllMissingLayers.bl_idname)
+
         layout.separator()
-        layout.operator(SaveStagedData.bl_idname)
+        layout.menu(ReLinkNodeLibMenu.bl_idname)
-        layout.operator(ReLinkNodes.bl_idname)
+        layout.operator(SaveNodeLib.bl_idname)
+
         layout.separator()
-        layout.operator(CleanAllCaches.bl_idname)
+        layout.menu(DangerZoneMenu.bl_idname)
+
+        layout.separator()
+        layout.menu(RenderSettingMenu.bl_idname)
+
+        layout.separator()
+        layout.operator(Help.bl_idname,
+                        icon=Help.bl_icon)
 
 
 def TOPBAR(self, context):
     layout = self.layout
+
+    if is_incompatible():
+        layout.menu(IncompatibleMenu.bl_idname)
+    else:
         layout.menu(BioxelNodesTopbarMenu.bl_idname)
 
 
+class NodeHeadMenu(bpy.types.Menu):
+    bl_idname = "BIOXELNODES_MT_NODE_HEAD"
+    bl_label = "Bioxel Nodes"
+    bl_icon = "FILE_VOLUME"
+
+    def draw(self, context):
+
+        layout = self.layout
+        layout.menu(AddLayerMenu.bl_idname,
+                    icon=AddLayerMenu.bl_icon)
+        layout.operator(SaveContainer.bl_idname)
+
+        layout.separator()
+        layout.operator(ContainerProps.bl_idname)
+        layout.menu(ExtractFromContainerMenu.bl_idname)
+
+        layout.separator()
+        layout.operator(SaveContainerLayersCache.bl_idname,
+                        icon=SaveContainerLayersCache.bl_icon)
+        layout.operator(RemoveContainerMissingLayers.bl_idname)
+
+        layout.separator()
+        layout.operator(AddLocator.bl_idname,
+                        icon=AddLocator.bl_icon)
+        layout.operator(AddSlicer.bl_idname,
+                        icon=AddSlicer.bl_icon)
+        layout.menu(AddCutterMenu.bl_idname)
+
+        layout.separator()
+        layout.menu(FetchLayerMenu.bl_idname)
+
+
+class NodeContextMenu(bpy.types.Menu):
+    bl_idname = "BIOXELNODES_MT_NODE_CONTEXT"
+    bl_label = "Bioxel Nodes"
+    bl_icon = "FILE_VOLUME"
+
+    def draw(self, context):
+        layout = self.layout
+        layout.operator(ExtractNodeMesh.bl_idname)
+        layout.operator(ExtractNodeShapeWire.bl_idname)
+        layout.operator(ExtractNodeBboxWire.bl_idname)
+
+        layout.separator()
+        layout.operator(SaveSelectedLayersCache.bl_idname,
+                        icon=SaveSelectedLayersCache.bl_icon)
+        layout.operator(RemoveSelectedLayers.bl_idname)
+
+        layout.separator()
+        layout.operator(RenameLayer.bl_idname,
+                        icon=RenameLayer.bl_icon)
+        layout.operator(RetimeLayer.bl_idname)
+        layout.operator(RelocateLayer.bl_idname)
+
+        layout.separator()
+        layout.operator(ResampleLayer.bl_idname,
+                        icon=ResampleLayer.bl_icon)
+        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)
+
+
+def NODE_CONTEXT(self, context):
+    if is_incompatible():
+        return
+
+    container_obj = context.object
+    is_geo_nodes = context.area.ui_type == "GeometryNodeTree"
+    is_container = get_container_obj(container_obj)
+
+    if not is_geo_nodes or not is_container:
+        return
+
+    layout = self.layout
+    layout.separator()
+    layout.menu(NodeContextMenu.bl_idname)
+
+
+def NODE_HEAD(self, context):
+    if is_incompatible():
+        return
+
+    container_obj = context.object
+    is_geo_nodes = context.area.ui_type == "GeometryNodeTree"
+    is_container = get_container_obj(container_obj)
+
+    if not is_geo_nodes or not is_container:
+        return
+
+    layout = self.layout
+    layout.separator()
+    layout.menu(NodeHeadMenu.bl_idname)
+
+
+def NODE_PROP(self, context):
+    if is_incompatible():
+        return
+
+    container_obj = context.object
+    is_geo_nodes = context.area.ui_type == "GeometryNodeTree"
+    is_container = get_container_obj(container_obj)
+    self.bl_label = "Group"
+
+    if not is_geo_nodes or not is_container:
+        return
+
+    if container_obj.modifiers[0].node_group != context.space_data.edit_tree:
+        return
+
+    self.bl_label = "Bioxel Nodes"
+
+    layer_list_UL = bpy.context.window_manager.bioxelnodes_layer_list_UL
+    layer_list = layer_list_UL.layer_list
+    layer_list.clear()
+
+    for layer_obj in get_container_layer_objs(container_obj):
+        layer_item = layer_list.add()
+        layer_item.label = get_layer_label(layer_obj)
+        layer_item.obj_name = layer_obj.name
+        layer_item.info_text = "\n".join([f"{prop}: {get_layer_prop_value(layer_obj, prop)}"
+                                          for prop in ["kind",
+                                                       "bioxel_size",
+                                                       "shape",
+                                                       "frame_count",
+                                                       "channel_count",
+                                                       "min", "max"]])
+
+    layout = self.layout
+    layout.label(text="Layer List")
+    split = layout.row()
+    split.template_list(listtype_name="BIOXELNODES_UL_layer_list",
+                        list_id="layer_list",
+                        dataptr=layer_list_UL,
+                        propname="layer_list",
+                        active_dataptr=layer_list_UL,
+                        active_propname="layer_list_active",
+                        item_dyntip_propname="info_text",
+                        rows=20)
+
+    # sidebar = split.column(align=True)
+    # sidebar.menu(AddLayerMenu.bl_idname,
+    #              icon=AddLayerMenu.bl_icon, text="")
+
+    # sidebar.operator(SaveContainerLayersCache.bl_idname,
+    #                  icon=SaveContainerLayersCache.bl_icon, text="")
+    # sidebar.operator(RemoveContainerMissingLayers.bl_idname,
+    #                  icon=RemoveContainerMissingLayers.bl_icon, text="")
+
+    # sidebar.separator()
+    # sidebar.operator(SaveSelectedLayersCache.bl_idname,
+    #                  icon=SaveSelectedLayersCache.bl_icon, text="")
+    # sidebar.operator(RemoveSelectedLayers.bl_idname,
+    #                  icon=RemoveSelectedLayers.bl_icon, text="")
+
+    # sidebar.separator()
+    # sidebar.operator(RenameLayer.bl_idname,
+    #                  icon=RenameLayer.bl_icon, text="")
+    # sidebar.operator(ResampleLayer.bl_idname,
+    #                  icon=ResampleLayer.bl_icon, text="")
+    # sidebar.operator(RetimeLayer.bl_idname,
+    #                  icon=RetimeLayer.bl_icon, text="")
+
+    # sidebar.separator()
+    # sidebar.operator(SignScalar.bl_idname,
+    #                  icon=SignScalar.bl_icon, text="")
+    # sidebar.operator(FillByThreshold.bl_idname,
+    #                  icon=FillByThreshold.bl_icon, text="")
+    # sidebar.operator(FillByRange.bl_idname,
+    #                  icon=FillByRange.bl_icon, text="")
+    # sidebar.operator(FillByLabel.bl_idname,
+    #                  icon=FillByLabel.bl_icon, text="")
+
+    # sidebar.separator()
+    # layout.separator()
+
+
+def VIEW3D_TOPBAR(self, context):
+    layout = self.layout
+    layout.operator(SliceViewer.bl_idname)
+
+
+node_menu = NodeMenu(
+    menu_items=MENU_ITEMS
+)
+
+
 def add():
-    bpy.types.TOPBAR_MT_file_import.append(TOPBAR_FILE_IMPORT)
+    node_menu.register()
-    # bpy.types.TOPBAR_MT_file_export.append(TOPBAR_FILE_EXPORT)
+    bpy.types.VIEW3D_HT_header.append(VIEW3D_TOPBAR)
-    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)
+    bpy.types.NODE_PT_node_tree_properties.prepend(NODE_PROP)
+    bpy.types.NODE_MT_editor_menus.append(NODE_HEAD)
+    bpy.types.NODE_MT_context_menu.append(NODE_CONTEXT)
 
 
 def remove():
-    bpy.types.TOPBAR_MT_file_import.remove(TOPBAR_FILE_IMPORT)
+    bpy.types.VIEW3D_HT_header.remove(VIEW3D_TOPBAR)
-    # 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)
+    bpy.types.NODE_PT_node_tree_properties.remove(NODE_PROP)
+    bpy.types.NODE_MT_editor_menus.remove(NODE_HEAD)
+    bpy.types.NODE_MT_context_menu.remove(NODE_CONTEXT)
+    node_menu.unregister()

bioxelnodes/node_menu.py

@@ -0,0 +1,87 @@
+import bpy
+from .operators.node import AddNode
+
+
+class NodeMenu():
+    def __init__(
+        self,
+        menu_items,
+    ) -> None:
+
+        self.menu_items = menu_items
+        self.class_prefix = f"BIOXELNODES_MT"
+        root_label = "Bioxel Nodes"
+        menu_classes = []
+        self._create_menu_class(
+            items=menu_items,
+            label=root_label,
+            menu_classes=menu_classes
+        )
+        self.menu_classes = menu_classes
+
+        idname = f"{self.class_prefix}_{root_label.replace(' ', '').upper()}"
+        icon = "FILE_VOLUME"
+
+        def drew_menu(self, context):
+            if (bpy.context.area.spaces[0].tree_type == 'GeometryNodeTree'):
+                layout = self.layout
+                layout.separator()
+                layout.menu(idname,
+                            icon=icon)
+        self.drew_menu = drew_menu
+
+    def _create_menu_class(self, menu_classes, items, label='CustomNodes', icon=0, idname_namespace=None):
+        idname_namespace = idname_namespace or self.class_prefix
+        idname = f"{idname_namespace}_{label.replace(' ', '').upper()}"
+
+        # create submenu class if item is menu.
+        for item in items:
+            item_items = item.get('items') if item != 'separator' else None
+            if item_items:
+                menu_class = self._create_menu_class(
+                    menu_classes=menu_classes,
+                    items=item_items,
+                    label=item.get('label') or 'CustomNodes',
+                    icon=item.get('icon') or 0,
+                    idname_namespace=idname
+                )
+                item['menu_class'] = menu_class
+
+        # create menu class
+        class Menu(bpy.types.Menu):
+            bl_idname = idname
+            bl_label = label
+
+            def draw(self, context):
+                layout = self.layout
+                for item in items:
+                    if item == "separator":
+                        layout.separator()
+                    elif item.get('menu_class'):
+                        layout.menu(
+                            item.get('menu_class').bl_idname,
+                            icon=item.get('icon') or 'NONE'
+                        )
+                    else:
+                        op = layout.operator(
+                            AddNode.bl_idname,
+                            text=item.get('label'),
+                            icon=item.get('icon') or 'NONE'
+                        )
+                        op.node_name = item['name']
+                        op.node_label = item.get('label') or ""
+                        op.node_description = item.get(
+                            'node_description') or ""
+
+        menu_classes.append(Menu)
+        return Menu
+
+    def register(self):
+        for cls in self.menu_classes:
+            bpy.utils.register_class(cls)
+        bpy.types.NODE_MT_add.append(self.drew_menu)
+
+    def unregister(self):
+        bpy.types.NODE_MT_add.remove(self.drew_menu)
+        for cls in reversed(self.menu_classes):
+            bpy.utils.unregister_class(cls)

bioxelnodes/nodes.py

@@ -1,228 +0,0 @@
-
-from pathlib import Path
-from .customnodes import CustomNodes
-
-NODE_FILE = "BioxelNodes_4.2"
-
-MENU_ITEMS = [
-    {
-        'label': 'Methods',
-        'icon': 'OUTLINER_DATA_VOLUME',
-        'items': [
-            {
-                'label': 'Mask by Threshold',
-                'icon': 'EMPTY_SINGLE_ARROW',
-                'node_type': 'BioxelNodes_MaskByThreshold',
-                'node_description': ''
-            },
-            {
-                'label': 'Mask by Range',
-                'icon': 'IPO_CONSTANT',
-                'node_type': 'BioxelNodes_MaskByRange',
-                'node_description': ''
-            },
-            {
-                'label': 'Mask by Label',
-                'icon': 'MESH_CAPSULE',
-                'node_type': 'BioxelNodes_MaskByLabel',
-                'node_description': ''
-            }
-        ]
-    },
-    {
-        'label': 'Shaders',
-        'icon': 'SHADING_RENDERED',
-        'items': [
-            {
-                'label': 'Membrane Shader',
-                'icon': 'NODE_MATERIAL',
-                'node_type': 'BioxelNodes_AssignMembraneShader',
-                'node_description': ''
-            },
-            {
-                'label': 'Solid Shader',
-                'icon': 'SHADING_SOLID',
-                'node_type': 'BioxelNodes_AssignSolidShader',
-                'node_description': ''
-            },
-            {
-                'label': 'Slime Shader',
-                'icon': 'OUTLINER_DATA_META',
-                'node_type': 'BioxelNodes_AssignSlimeShader',
-                'node_description': ''
-            },
-            {
-                'label': 'Volume Shader',
-                'icon': 'VOLUME_DATA',
-                'node_type': 'BioxelNodes_AssignVolumeShader',
-                'node_description': ''
-            },
-            {
-                'label': 'Universal Shader',
-                'icon': 'MATSHADERBALL',
-                'node_type': 'BioxelNodes_AssignUniversalShader',
-                'node_description': ''
-            }
-        ]
-    },
-    {
-        'label': 'Colors',
-        'icon': 'COLOR',
-        'items': [
-            {
-                'label': 'Color Presets',
-                'icon': 'COLOR',
-                'node_type': 'BioxelNodes_ColorPresets',
-                'node_description': ''
-            },
-            {
-                'label': 'Color Presets MRI',
-                'icon': 'COLOR',
-                'node_type': 'BioxelNodes_ColorPresets_MRI',
-                'node_description': ''
-            },
-            "separator",
-            {
-                'label': 'Color Ramp 2',
-                'icon': 'IPO_QUAD',
-                'node_type': 'BioxelNodes_SetColorRamp2',
-                'node_description': ''
-            },
-            {
-                'label': 'Color Ramp 3',
-                'icon': 'IPO_CUBIC',
-                'node_type': 'BioxelNodes_SetColorRamp3',
-                'node_description': ''
-            },
-            {
-                'label': 'Color Ramp 4',
-                'icon': 'IPO_QUART',
-                'node_type': 'BioxelNodes_SetColorRamp4',
-                'node_description': ''
-            },
-            {
-                'label': 'Color Ramp 5',
-                'icon': 'IPO_QUINT',
-                'node_type': 'BioxelNodes_SetColorRamp5',
-                'node_description': ''
-            }
-        ]
-    },
-    {
-        'label': 'Cutters',
-        'icon': 'MOD_BEVEL',
-        'items': [
-            {
-                'label': 'Cut',
-                'icon': 'MOD_BEVEL',
-                'node_type': 'BioxelNodes_Cut',
-                'node_description': ''
-            },
-            "separator",
-            {
-                'label': 'Primitive Cutter',
-                'icon': 'MOD_LINEART',
-                'node_type': 'BioxelNodes_PrimitiveCutter',
-                'node_description': ''
-            },
-            "separator",
-            {
-                'label': 'Plane Cutter',
-                'icon': 'MESH_PLANE',
-                'node_type': 'BioxelNodes_PlaneObjectCutter',
-                'node_description': ''
-            },
-            {
-                'label': 'Cylinder Cutter',
-                'icon': 'MESH_CYLINDER',
-                'node_type': 'BioxelNodes_CylinderObjectCutter',
-                'node_description': '',
-            },
-            {
-                'label': 'Cube Cutter',
-                'icon': 'MESH_CUBE',
-                'node_type': 'BioxelNodes_CubeObjectCutter',
-                'node_description': '',
-            },
-            {
-                'label': 'Sphere Cutter',
-                'icon': 'MESH_UVSPHERE',
-                'node_type': 'BioxelNodes_SphereObjectCutter',
-                'node_description': '',
-            },
-            {
-                'label': 'Pie Cutter',
-                'icon': 'MESH_CONE',
-                'node_type': 'BioxelNodes_PieObjectCutter',
-                'node_description': '',
-            }
-        ]
-    },
-    {
-        'label': 'Utils',
-        'icon': 'MODIFIER',
-        'items': [
-            {
-                'label': 'Join Component',
-                'icon': 'CONSTRAINT_BONE',
-                'node_type': 'BioxelNodes_JoinComponent',
-                'node_description': ''
-            },
-            "separator",
-            {
-                'label': 'Pick Mesh',
-                'icon': 'OUTLINER_OB_MESH',
-                'node_type': 'BioxelNodes_PickMesh',
-                'node_description': ''
-            },
-            {
-                'label': 'Pick Volume',
-                'icon': 'OUTLINER_OB_VOLUME',
-                'node_type': 'BioxelNodes_PickVolume',
-                'node_description': ''
-            },
-            {
-                'label': 'Pick Bbox Wire',
-                'icon': 'MESH_CUBE',
-                'node_type': 'BioxelNodes_PickBboxWire',
-                'node_description': ''
-            },
-            "separator",
-            {
-                'label': 'Inflate',
-                'icon': 'OUTLINER_OB_META',
-                'node_type': 'BioxelNodes_M_Inflate',
-                'node_description': ''
-            },
-            {
-                'label': 'Smooth',
-                'icon': 'MOD_SMOOTH',
-                'node_type': 'BioxelNodes_M_Smooth',
-                'node_description': ''
-            },
-            {
-                'label': 'Remove Small Island',
-                'icon': 'FORCE_LENNARDJONES',
-                'node_type': 'BioxelNodes_M_RemoveSmallIsland',
-                'node_description': ''
-            }
-        ]
-    }
-]
-
-
-custom_nodes = CustomNodes(
-    menu_items=MENU_ITEMS,
-    nodes_file=Path(__file__).parent / f"assets/Nodes/{NODE_FILE}.blend",
-    class_prefix="BIOXELNODES_MT_NODES",
-    root_label='Bioxel Nodes',
-    root_icon="FILE_VOLUME",
-)
-
-
-def register():
-    custom_nodes.register()
-
-
-def unregister():
-    custom_nodes.unregister()

bioxelnodes/operators/container.py

@@ -3,13 +3,17 @@ import bpy
 
 import bmesh
 
-from ..nodes import custom_nodes
+from ..constants import COMPONENT_OUTPUT_NODES
+from ..utils import get_cache_dir, get_use_link, select_object
 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
-from ..bioxelutils.container import (container_to_obj, obj_to_container,
+from ..bioxelutils.node import add_node_to_graph
-                                     get_container_objs_from_selection)
+from ..bioxelutils.common import (get_container_layer_objs, get_container_obj, get_node_type,
-from ..bioxelutils.node import get_nodes_by_type, move_node_between_nodes, move_node_to_node
+                                  get_nodes_by_type, get_output_node, is_missing_layer,
-from .utils import change_render_setting, get_cache_dir, get_preferences, select_object
+                                  move_node_between_nodes,
+                                  move_node_to_node,
+                                  get_all_layer_objs)
+from .layer import RemoveLayers, SaveLayersCache
 
 
 class SaveContainer(bpy.types.Operator):
@@ -23,19 +27,14 @@ class SaveContainer(bpy.types.Operator):
 
     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()
+        container_obj = get_container_obj(context.object)
 
-        if len(container_objs) == 0:
+        if container_obj is None:
             self.report({"WARNING"}, "Cannot find any bioxel container.")
             return {'FINISHED'}
 
-        container = obj_to_container(container_objs[0])
+        container = obj_to_container(container_obj)
         save_path = f"{self.filepath.split('.')[0]}.bioxel"
         save_container(container, save_path, overwrite=True)
 
@@ -65,11 +64,12 @@ class LoadContainer(bpy.types.Operator):
 
         container_obj = container_to_obj(container,
                                          scene_scale=0.01,
-                                         cache_dir=get_cache_dir(context))
+                                         cache_dir=get_cache_dir())
         select_object(container_obj)
 
         if is_first_import:
-            change_render_setting(context)
+            bpy.ops.bioxelnodes.render_setting_preset('EXEC_DEFAULT',
+                                                      preset="preview_c")
 
         self.report({"INFO"}, f"Successfully load {load_path}")
         return {'FINISHED'}
@@ -79,39 +79,63 @@ class LoadContainer(bpy.types.Operator):
         return {'RUNNING_MODAL'}
 
 
-class PickObject():
+class ExtractNodeObject():
     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()
+        container_obj = get_container_obj(context.object)
 
-        if len(container_objs) == 0:
+        if container_obj is None:
             self.report({"WARNING"}, "Cannot find any bioxel container.")
             return {'FINISHED'}
 
-        container_obj = container_objs[0]
+        # nodes = [node for node in context.selected_nodes
+        #          if get_node_type(node).removeprefix("BioxelNodes_") in COMPONENT_OUTPUT_NODES]
+
+        if len(context.selected_nodes) == 0:
+            self.report({"WARNING"}, "No node selected.")
+            return {'FINISHED'}
+
+        selected_node = context.selected_nodes[0]
+        container_node_group = container_obj.modifiers[0].node_group
+
+        container_output_node = get_output_node(container_node_group)
+
+        if len(container_output_node.inputs[0].links) == 0:
+            pre_socket = None
+        else:
+            pre_socket = container_output_node.inputs[0].links[0].from_socket
+
+        container_node_group.links.new(selected_node.outputs[0],
+                                       container_output_node.inputs[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}"
+        obj.name = f"{container_obj.name}_{self.object_type}"
 
         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,
+        fetch_mesh_node = add_node_to_graph(f"Fetch{self.object_type}",
-                                               f"BioxelNodes_Pick{self.object_type}")
+                                            node_group,
+                                            node_label=f"Fetch {self.object_type}",
+                                            use_link=get_use_link())
 
-        pick_mesh_node.inputs[0].default_value = container_obj
+        fetch_mesh_node.inputs[0].default_value = container_obj
-        node_group.links.new(pick_mesh_node.outputs[0], output_node.inputs[0])
+        node_group.links.new(fetch_mesh_node.outputs[0], output_node.inputs[0])
+
+        for modifier in obj.modifiers:
+            bpy.ops.object.modifier_apply(modifier=modifier.name)
+
+        obj.data.materials.clear()
+
+        if pre_socket:
+            container_node_group.links.new(pre_socket,
+                                           container_output_node.inputs[0])
 
         select_object(obj)
 
@@ -120,71 +144,146 @@ class PickObject():
         return {'FINISHED'}
 
 
-class PickMesh(bpy.types.Operator, PickObject):
+class ExtractNodeMesh(bpy.types.Operator, ExtractNodeObject):
-    bl_idname = "bioxelnodes.pick_mesh"
+    bl_idname = "bioxelnodes.extract_node_mesh"
-    bl_label = "Pick Mesh"
+    bl_label = "Extract Mesh"
-    bl_description = "Pick Container Mesh"
+    bl_description = "Extract Mesh"
+    bl_icon = "OUTLINER_OB_MESH"
     object_type = "Mesh"
 
 
-class PickVolume(bpy.types.Operator, PickObject):
+class ExtractNodeShapeWire(bpy.types.Operator, ExtractNodeObject):
-    bl_idname = "bioxelnodes.pick_volume"
+    bl_idname = "bioxelnodes.extract_node_shape_wire"
-    bl_label = "Pick Volume"
+    bl_label = "Extract Shape Wire"
-    bl_description = "Pick Container Volume"
+    bl_description = "Extract Shape Wire"
-    object_type = "Volume"
+    bl_icon = "FILE_VOLUME"
+    object_type = "ShapeWire"
 
 
-class PickBboxWire(bpy.types.Operator, PickObject):
+class ExtractNodeBboxWire(bpy.types.Operator, ExtractNodeObject):
-    bl_idname = "bioxelnodes.pick_bbox_wire"
+    bl_idname = "bioxelnodes.extract_node_bbox_wire"
-    bl_label = "Pick Bbox Wire"
+    bl_label = "Extract Bbox Wire"
-    bl_description = "Pick Container Bbox Wire"
+    bl_description = "Extract Bbox Wire"
+    bl_icon = "MESH_CUBE"
+    object_type = "BboxWire"
+
+
+class ExtractObject():
+    bl_options = {'UNDO'}
+
+    def execute(self, context):
+        container_obj = get_container_obj(context.object)
+
+        if container_obj is None:
+            self.report({"WARNING"}, "Cannot find any bioxel container.")
+            return {'FINISHED'}
+
+        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"{container_obj.name}_{self.object_type}"
+
+        bpy.ops.node.new_geometry_nodes_modifier()
+        modifier = obj.modifiers[0]
+        node_group = modifier.node_group
+
+        output_node = get_output_node(node_group)
+
+        fetch_mesh_node = add_node_to_graph(f"Fetch{self.object_type}",
+                                            node_group,
+                                            node_label=f"Fetch {self.object_type}",
+                                            use_link=get_use_link())
+
+        fetch_mesh_node.inputs[0].default_value = container_obj
+
+        if self.object_type == "Mesh":
+            node_group.links.new(
+                fetch_mesh_node.outputs[0], output_node.inputs[0])
+        else:
+            curve_to_mesh_node = node_group.nodes.new(
+                "GeometryNodeCurveToMesh")
+            node_group.links.new(
+                fetch_mesh_node.outputs[0], curve_to_mesh_node.inputs[0])
+            node_group.links.new(
+                curve_to_mesh_node.outputs[0], output_node.inputs[0])
+
+        for modifier in obj.modifiers:
+            bpy.ops.object.modifier_apply(modifier=modifier.name)
+
+        obj.data.materials.clear()
+
+        select_object(obj)
+
+        self.report({"INFO"}, f"Successfully picked")
+
+        return {'FINISHED'}
+
+
+class ExtractMesh(bpy.types.Operator, ExtractObject):
+    bl_idname = "bioxelnodes.extract_mesh"
+    bl_label = "Extract Mesh"
+    bl_description = "Extract Mesh"
+    bl_icon = "OUTLINER_OB_MESH"
+    object_type = "Mesh"
+
+
+class ExtractShapeWire(bpy.types.Operator, ExtractObject):
+    bl_idname = "bioxelnodes.extract_shape_wire"
+    bl_label = "Extract Shape Wire"
+    bl_description = "Extract Shape Wire"
+    bl_icon = "FILE_VOLUME"
+    object_type = "ShapeWire"
+
+
+class ExtractBboxWire(bpy.types.Operator, ExtractObject):
+    bl_idname = "bioxelnodes.extract_bbox_wire"
+    bl_label = "Extract Bbox Wire"
+    bl_description = "Extract Bbox Wire"
+    bl_icon = "MESH_CUBE"
     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()
+        container_obj = get_container_obj(context.object)
 
-        if len(container_objs) == 0:
+        if container_obj is None:
             self.report({"WARNING"}, "Cannot find any bioxel container.")
             return {'FINISHED'}
-
+        # TODO: do not use operator to create obj
-        container_obj = container_objs[0]
+        if self.cutter_type == "plane":
-
-        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":
+        elif self.cutter_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":
+        elif self.cutter_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":
+        elif self.cutter_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":
+        elif self.cutter_type == "pie":
-            node_type = "BioxelNodes_PieObjectCutter"
+            bpy.ops.mesh.primitive_plane_add(
+                size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
+            pie_obj = bpy.context.active_object
+            orig_data = pie_obj.data
+
             # Create mesh
             pie_mesh = bpy.data.meshes.new('Pie')
+            pie_obj.data = pie_mesh
+            bpy.data.meshes.remove(orig_data)
 
-            # Create object
+            # # Create object
-            pie = bpy.data.objects.new('Pie', pie_mesh)
+            # pie = bpy.data.objects.new('Pie', pie_mesh)
+
+            # # Link object to scene
+            # bpy.context.scene.collection.objects.link(pie)
 
-            # 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
@@ -208,9 +307,22 @@ class AddCutter():
 
             # Finish up, write the bmesh back to the mesh
             bm.to_mesh(pie_mesh)
-            bpy.context.view_layer.objects.active = pie
+            # bpy.context.view_layer.objects.active = pie
 
         cutter_obj = bpy.context.active_object
+
+        # vcos = [container_obj.matrix_world @
+        #         v.co for v in container_obj.data.vertices]
+
+        # def find_center(l): return (max(l) + min(l)) / 2
+
+        # x, y, z = [[v[i] for v in vcos] for i in range(3)]
+        # center = [find_center(axis) for axis in [x, y, z]]
+
+        # cutter_obj.location = center
+        name = f"{self.cutter_type.capitalize()}_Cutter"
+        cutter_obj.name = name
+        cutter_obj.data.name = name
         cutter_obj.visible_camera = False
         cutter_obj.visible_diffuse = False
         cutter_obj.visible_glossy = False
@@ -219,17 +331,29 @@ class AddCutter():
         cutter_obj.visible_shadow = False
         cutter_obj.hide_render = True
         cutter_obj.display_type = 'WIRE'
+        cutter_obj.lineart.usage = 'EXCLUDE'
+
+        select_object(container_obj)
 
         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')
+            cutter_node = add_node_to_graph("ObjectCutter",
+                                            node_group,
+                                            node_label=f"{self.cutter_type.capitalize()} Cutter",
+                                            use_link=get_use_link())
+            cutter_node.inputs[0].default_value = self.cutter_type.capitalize()
+            cutter_node.inputs[1].default_value = cutter_obj
+
+            cut_node = add_node_to_graph("Cut",
+                                         node_group,
+                                         use_link=get_use_link())
+
+            output_node = get_output_node(node_group)
+
             if len(output_node.inputs[0].links) == 0:
                 node_group.links.new(cut_node.outputs[0],
                                      output_node.inputs[0])
@@ -247,10 +371,13 @@ class AddCutter():
                                  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))
+            bpy.ops.bioxelnodes.add_node('EXEC_DEFAULT',
-            select_object(container_obj)
+                                         node_name="ObjectCutter",
+                                         node_label=name)
+            node = bpy.context.active_node
+            node.inputs[0].default_value = self.cutter_type.capitalize()
+            node.inputs[1].default_value = cutter_obj
 
         return {'FINISHED'}
 
@@ -258,33 +385,243 @@ class AddCutter():
 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_description = "Add a plane cutter to current container"
-    object_type = "plane"
+    bl_icon = "MESH_PLANE"
+    cutter_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_description = "Add a cylinder cutter to current container"
-    object_type = "cylinder"
+    bl_icon = "MESH_CYLINDER"
+    cutter_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_description = "Add a cube cutter to current container"
-    object_type = "cube"
+    bl_icon = "MESH_CUBE"
+    cutter_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_description = "Add a sphere cutter to current container"
-    object_type = "sphere"
+    bl_icon = "MESH_UVSPHERE"
+    cutter_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_description = "Add a pie cutter to current container"
-    object_type = "pie"
+    bl_icon = "MESH_CONE"
+    cutter_type = "pie"
+
+
+class AddSlicer(bpy.types.Operator):
+    bl_idname = "bioxelnodes.add_slicer"
+    bl_label = "Add a Slicer"
+    bl_description = "Add a slicer to current container"
+    bl_icon = "TEXTURE"
+    bl_options = {'UNDO'}
+
+    def execute(self, context):
+        container_obj = get_container_obj(context.object)
+
+        if container_obj is None:
+            self.report({"WARNING"}, "Cannot find any bioxel container.")
+            return {'FINISHED'}
+
+        bpy.ops.mesh.primitive_plane_add(size=2,
+                                         enter_editmode=False,
+                                         align='WORLD',
+                                         location=(0, 0, 0),
+                                         scale=(1, 1, 1))
+
+        slicer_obj = bpy.context.active_object
+        slicer_obj.name = "Slicer"
+        slicer_obj.data.name = "Slicer"
+
+        slicer_obj.visible_camera = False
+        slicer_obj.visible_diffuse = False
+        slicer_obj.visible_glossy = False
+        slicer_obj.visible_transmission = False
+        slicer_obj.visible_volume_scatter = False
+        slicer_obj.visible_shadow = False
+        slicer_obj.hide_render = True
+        slicer_obj.display_type = 'WIRE'
+        slicer_obj.lineart.usage = 'EXCLUDE'
+
+        select_object(container_obj)
+
+        modifier = container_obj.modifiers[0]
+        node_group = modifier.node_group
+
+        slice_node = add_node_to_graph("Slice",
+                                       node_group,
+                                       use_link=get_use_link())
+
+        slice_node.inputs[1].default_value = slicer_obj
+
+        output_node = get_output_node(node_group)
+
+        if len(output_node.inputs[0].links) == 0:
+            node_group.links.new(slice_node.outputs[0],
+                                 output_node.inputs[0])
+            move_node_to_node(slice_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],
+                                 slice_node.inputs[0])
+            node_group.links.new(slice_node.outputs[0],
+                                 output_node.inputs[0])
+            move_node_between_nodes(slice_node,
+                                    [pre_output_node, output_node])
+
+        return {'FINISHED'}
+
+
+class AddLocator(bpy.types.Operator):
+    bl_idname = "bioxelnodes.add_locator"
+    bl_label = "Add a Locator"
+    bl_description = "Add a locator to current container"
+    bl_icon = "EMPTY_AXIS"
+    bl_options = {'UNDO'}
+
+    def execute(self, context):
+        container_obj = get_container_obj(context.object)
+
+        if container_obj is None:
+            self.report({"WARNING"}, "Cannot find any bioxel container.")
+            return {'FINISHED'}
+
+        bpy.ops.object.empty_add(type='ARROWS',
+                                 align='WORLD',
+                                 location=(0, 0, 0),
+                                 scale=(1, 1, 1))
+
+        locator_obj = bpy.context.active_object
+        locator_obj.name = "Locator"
+        select_object(container_obj)
+
+        modifier = container_obj.modifiers[0]
+        node_group = modifier.node_group
+
+        parent_node = add_node_to_graph("TransformParent",
+                                        node_group,
+                                        node_label="Transform Parent",
+                                        use_link=get_use_link())
+
+        parent_node.inputs[1].default_value = locator_obj
+
+        output_node = get_output_node(node_group)
+
+        if len(output_node.inputs[0].links) == 0:
+            node_group.links.new(parent_node.outputs[0],
+                                 output_node.inputs[0])
+            move_node_to_node(parent_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],
+                                 parent_node.inputs[0])
+            node_group.links.new(parent_node.outputs[0],
+                                 output_node.inputs[0])
+            move_node_between_nodes(parent_node,
+                                    [pre_output_node, output_node])
+
+        return {'FINISHED'}
+
+
+class ContainerProps(bpy.types.Operator):
+    bl_idname = "bioxelnodes.container_props"
+    bl_label = "Change Container Properties"
+    bl_description = "Change current ontainer properties"
+    bl_icon = "FILE_TICK"
+
+    scene_scale: bpy.props.FloatProperty(name="Scene Scale",
+                                         soft_min=0.0001, soft_max=10.0,
+                                         min=1e-6, max=1e6,
+                                         default=0.01)  # type: ignore
+
+    step_size: bpy.props.FloatProperty(name="Step Size",
+                                       soft_min=0.1, soft_max=100.0,
+                                       min=0.1, max=1e2,
+                                       default=1)  # type: ignore
+
+    def execute(self, context):
+        container_obj = get_container_obj(context.object)
+
+        if container_obj is None:
+            self.report({"WARNING"}, "Cannot find any bioxel container.")
+            return {'FINISHED'}
+
+        container_obj.scale[0] = self.scene_scale
+        container_obj.scale[1] = self.scene_scale
+        container_obj.scale[2] = self.scene_scale
+        container_obj["scene_scale"] = self.scene_scale
+        container_obj["step_size"] = self.step_size
+
+        for layer_obj in get_container_layer_objs(container_obj):
+            layer_obj.data.render.space = 'WORLD'
+            layer_obj.data.render.step_size = self.scene_scale * self.step_size
+
+        return {'FINISHED'}
+
+    def invoke(self, context, event):
+        container_obj = get_container_obj(context.object)
+
+        if container_obj is None:
+            return self.execute(context)
+        else:
+            self.scene_scale = container_obj.get("scene_scale") or 0.01
+            self.step_size = container_obj.get("step_size") or 1
+            context.window_manager.invoke_props_dialog(self)
+            return {'RUNNING_MODAL'}
+
+
+def get_container_layers(context, layer_filter=None):
+    def _layer_filter(layer_obj, context):
+        return True
+
+    layer_filter = layer_filter or _layer_filter
+    container_obj = context.object
+    layer_objs = get_container_layer_objs(container_obj)
+    return [obj for obj in layer_objs if layer_filter(obj, context)]
+
+
+class SaveContainerLayersCache(bpy.types.Operator, SaveLayersCache):
+    bl_idname = "bioxelnodes.save_container_layers_cache"
+    bl_label = "Save Container Layers' Cache"
+    bl_description = "Save all current container layers' cache to directory."
+    bl_icon = "FILE_TICK"
+
+    success_msg = "Successfully saved all container layers."
+
+    def get_layers(self, context):
+        def is_not_missing(layer_obj, context):
+            return not is_missing_layer(layer_obj)
+        return get_container_layers(context, is_not_missing)
+
+
+class RemoveContainerMissingLayers(bpy.types.Operator, RemoveLayers):
+    bl_idname = "bioxelnodes.remove_container_missing_layers"
+    bl_label = "Remove Container Missing Layers"
+    bl_description = "Remove all current container missing layers"
+    bl_icon = "BRUSH_DATA"
+
+    success_msg = "Successfully removed all container missing layers."
+
+    def get_layers(self, context):
+        def is_missing(layer_obj, context):
+            return is_missing_layer(layer_obj)
+        return get_container_layers(context, is_missing)
+
+    def invoke(self, context, event):
+        context.window_manager.invoke_confirm(self,
+                                              event,
+                                              message=f"Are you sure to remove all **Missing** layers?")
+        return {'RUNNING_MODAL'}

bioxelnodes/operators/io.py

@@ -5,20 +5,20 @@ 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.common import (get_all_layer_objs, get_container_obj,
-from ..bioxelutils.layer import (get_all_layer_objs,
+                                  get_layer_obj, is_incompatible)
-                                 get_layer_obj)
 from ..bioxelutils.container import (Container,
                                      add_layers,
-                                     container_to_obj,
+                                     container_to_obj)
-                                     get_container_objs_from_selection)
+from ..bioxel.layer import Layer
 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)
+from ..utils import (get_cache_dir,
+                     progress_update, progress_bar,
+                     select_object)
 
 # 3rd-party
 import SimpleITK as sitk
@@ -57,7 +57,7 @@ class ImportVolumetricData():
 
     filepath: bpy.props.StringProperty(subtype="FILE_PATH")  # type: ignore
 
-    read_as = "scalar"
+    read_as = "SCALAR"
 
     def execute(self, context):
         data_path = Path(self.filepath).resolve()
@@ -78,18 +78,28 @@ class ImportVolumetricData():
         return {'RUNNING_MODAL'}
 
 
-class ImportAsScalarLayer(bpy.types.Operator, ImportVolumetricData):
+class ImportAsScalar(bpy.types.Operator, ImportVolumetricData):
-    bl_idname = "bioxelnodes.import_as_scalar_layer"
+    bl_idname = "bioxelnodes.import_as_scalar"
     bl_label = "Import as Scalar"
     bl_description = "Import Volumetric Data to Container as Scalar"
-    read_as = "scalar"
+    bl_icon = "EVENT_S"
+    read_as = "SCALAR"
 
 
-class ImportAsLabelLayer(bpy.types.Operator, ImportVolumetricData):
+class ImportAsLabel(bpy.types.Operator, ImportVolumetricData):
-    bl_idname = "bioxelnodes.import_as_label_layer"
+    bl_idname = "bioxelnodes.import_as_label"
     bl_label = "Import as Label"
     bl_description = "Import Volumetric Data to Container as Label"
-    read_as = "label"
+    bl_icon = "EVENT_L"
+    read_as = "LABEL"
+
+
+class ImportAsColor(bpy.types.Operator, ImportVolumetricData):
+    bl_idname = "bioxelnodes.import_as_color"
+    bl_label = "Import as Color"
+    bl_description = "Import Volumetric Data to Container as Color"
+    bl_icon = "EVENT_C"
+    read_as = "COLOR"
 
 
 class BIOXELNODES_FH_ImportVolumetricData(bpy.types.FileHandler):
@@ -100,7 +110,16 @@ class BIOXELNODES_FH_ImportVolumetricData(bpy.types.FileHandler):
 
     @classmethod
     def poll_drop(cls, context):
-        return (context.area and context.area.type == 'VIEW_3D')
+        if not context.area:
+            return False
+
+        if context.area.type == 'VIEW_3D':
+            return True
+        elif context.area.type == 'NODE_EDITOR':
+            container_obj = get_container_obj(context.object)
+            return container_obj is not None
+        else:
+            return False
 
 
 def get_series_ids(self, context):
@@ -123,9 +142,10 @@ class ParseVolumetricData(bpy.types.Operator):
     bl_options = {'UNDO'}
 
     meta = None
+    label_count = 0
+    dtype = None
     thread = None
     _timer = None
-    container_obj_name = ""
 
     progress: bpy.props.FloatProperty(name="Progress",
                                       options={"SKIP_SAVE"},
@@ -134,15 +154,18 @@ class ParseVolumetricData(bpy.types.Operator):
     filepath: bpy.props.StringProperty(subtype="FILE_PATH")  # type: ignore
 
     skip_read_as: bpy.props.BoolProperty(name="Skip Read As",
-                                         default=False)  # type: ignore
+                                         default=False,
+                                         options={"SKIP_SAVE"})  # type: ignore
 
     skip_series_select: bpy.props.BoolProperty(name="Skip Sries Select",
-                                               default=True)  # type: ignore
+                                               default=True,
+                                               options={"SKIP_SAVE"})  # type: ignore
 
     read_as: bpy.props.EnumProperty(name="Read as",
-                                    default="scalar",
+                                    default="SCALAR",
-                                    items=[("scalar", "Scalar", ""),
+                                    items=[("SCALAR", "Scalar", ""),
-                                           ("label", "Labels", "")])  # type: ignore
+                                           ("LABEL", "Label", ""),
+                                           ("COLOR", "Color", "")])  # type: ignore
 
     series_id: bpy.props.EnumProperty(name="Select Series",
                                       items=get_series_ids)  # type: ignore
@@ -151,6 +174,15 @@ class ParseVolumetricData(bpy.types.Operator):
         type=BIOXELNODES_Series)  # type: ignore
 
     def execute(self, context):
+        if is_incompatible():
+            self.report({"ERROR"},
+                        "Current addon verison is not compatible to this file. If you insist on editing this file please keep the same addon version")
+            return {'CANCELLED'}
+
+        if not self.filepath:
+            self.report({"WARNING"}, "No file selected.")
+            return {'CANCELLED'}
+
         data_path = Path(self.filepath).resolve()
         ext = get_ext(data_path)
         if ext not in SUPPORT_EXTS:
@@ -180,6 +212,8 @@ class ParseVolumetricData(bpy.types.Operator):
                 return
 
             self.meta = meta
+            self.label_count = int(np.max(data))
+            self.dtype = data.dtype
 
         # Init cancel flag
         self.is_cancelled = False
@@ -205,7 +239,7 @@ class ParseVolumetricData(bpy.types.Operator):
         # Check if user press 'ESC'
         if event.type == 'ESC':
             self.is_cancelled = True
-            progress_update(context, 0, "Canceling...")
+            progress_update(context, 0.0, "Canceling...")
             return {'PASS_THROUGH'}
 
         # Check if is the timer time
@@ -225,6 +259,7 @@ class ParseVolumetricData(bpy.types.Operator):
         context.window_manager.event_timer_remove(self._timer)
         # Remove the progress bar from status bar
         bpy.types.STATUSBAR_HT_header.remove(progress_bar)
+        progress_update(context, 1.0)
 
         # Check if thread is cancelled by user
         if self.is_cancelled:
@@ -244,25 +279,61 @@ class ParseVolumetricData(bpy.types.Operator):
         for key, value in self.meta.items():
             print(f"{key}: {value}")
 
+        if self.read_as == "LABEL":
+            if self.label_count > 100 or self.dtype.kind not in ["i", "u"]:
+                self.report({"ERROR"}, "Invaild label data.")
+                return {'CANCELLED'}
+
+            if self.label_count == 0:
+                self.report({"ERROR"}, "Get no label.")
+                return {'CANCELLED'}
+
         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)
+        min_log10 = math.floor(math.log10(min(*orig_spacing)))
+        max_log10 = math.floor(math.log10(max(*orig_spacing)))
+        # min_space = min(*orig_spacing)
+        # max_space = max(*orig_spacing)
+
+        if orig_spacing[2] == 1 and min_log10 < -1:
+            orig_spacing = (orig_spacing[0] * math.pow(10, -min_log10-2),
+                            orig_spacing[1] * math.pow(10, -min_log10-2),
+                            1)
+        elif min_log10 > 0:
+            orig_spacing = (orig_spacing[0] * math.pow(10, -min_log10-1),
+                            orig_spacing[1] * math.pow(10, -min_log10-1),
+                            orig_spacing[2] * math.pow(10, -min_log10-1))
+        elif max_log10 < 0:
+            orig_spacing = (orig_spacing[0] * math.pow(10, -max_log10-1),
+                            orig_spacing[1] * math.pow(10, -max_log10-1),
+                            orig_spacing[2] * math.pow(10, -max_log10-1))
+
+        bioxel_size = max(min(*orig_spacing), 1.0)
+
+        layer_shape = get_layer_shape(bioxel_size,
+                                      orig_shape,
+                                      orig_spacing)
         layer_size = get_layer_size(layer_shape,
-                                    bioxel_size)
+                                    bioxel_size,
-        log10 = math.floor(math.log10(max(*layer_size)))
+                                    0.01)
-        log10 = max(1, log10)
+        min_log10 = math.floor(math.log10(min(*layer_size)))
-        log10 = min(3, log10)
+        max_log10 = math.floor(math.log10(max(*layer_size)))
-        scene_scale = math.pow(10, -log10)
 
-        if self.container_obj_name:
+        if min_log10 > 0:
-            container_obj = bpy.data.objects.get(self.container_obj_name)
+            scene_scale = math.pow(10, -min_log10-2)
+        elif max_log10 < 0:
+            scene_scale = math.pow(10, -max_log10-2)
+        else:
+            scene_scale = 0.01
+
+        if context.area.type == "NODE_EDITOR":
+            container_obj = context.object
             container_name = container_obj.name
+            container_obj_name = container_name
         else:
             container_name = self.meta['name']
+            container_obj_name = ""
 
         series_id = self.series_id if self.series_id != "empty" else ""
         bpy.ops.bioxelnodes.import_volumetric_data_dialog(
@@ -276,8 +347,9 @@ class ParseVolumetricData(bpy.types.Operator):
             series_id=series_id,
             frame_count=self.meta['frame_count'],
             channel_count=self.meta['channel_count'],
-            container_obj_name=self.container_obj_name,
+            container_obj_name=container_obj_name,
             read_as=self.read_as,
+            label_count=self.label_count,
             scene_scale=scene_scale
         )
 
@@ -285,18 +357,22 @@ class ParseVolumetricData(bpy.types.Operator):
         return {'FINISHED'}
 
     def invoke(self, context, event):
-        if not self.filepath:
+        # why not report in execute?
+        # If this operator is executing, a new execute will when pre-one done.
+        if context.window_manager.bioxelnodes_progress_factor < 1:
+            print("A process is executing, please wait for it to finish.")
             return {'CANCELLED'}
 
+        if not self.filepath:
+            return self.execute(context)
+
         data_path = Path(self.filepath).resolve()
         ext = get_ext(data_path)
 
-        container_objs = get_container_objs_from_selection()
+        if context.area.type == "NODE_EDITOR":
-        if len(container_objs) > 0:
+            title = f"Add to **{context.object.name}**"
-            self.container_obj_name = container_objs[0].name
+        else:
-
+            title = "Init a Container"
-        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:
@@ -319,6 +395,7 @@ class ParseVolumetricData(bpy.types.Operator):
                 def get_meta(key):
                     try:
                         stirng = single.GetMetaData(key).removesuffix(" ")
+                        stirng.encode('utf-8')
                         if stirng in ["No study description",
                                       "No series description",
                                       ""]:
@@ -344,13 +421,15 @@ class ParseVolumetricData(bpy.types.Operator):
                 if series_id == "":
                     series_id = "empty"
 
-                series_items[series_id] = "{:<20} {:>1}".format(f"{study_description}>{series_description}({series_modality})",
+                label = "{:<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_items[series_id] = label
+
+            for series_id, label in series_items.items():
                 series_item = self.series_ids.add()
-                series_item.id = key
+                series_item.id = series_id
-                series_item.label = value
+                series_item.label = label
 
             if len(series_items.keys()) > 1:
                 self.skip_series_select = False
@@ -365,8 +444,7 @@ class ParseVolumetricData(bpy.types.Operator):
                 return {'CANCELLED'}
 
         if self.skip_read_as:
-            self.execute(context)
+            return self.execute(context)
-            return {'RUNNING_MODAL'}
         else:
             context.window_manager.invoke_props_dialog(self,
                                                        width=400,
@@ -384,17 +462,17 @@ class ParseVolumetricData(bpy.types.Operator):
             layout.prop(self, "series_id")
 
 
-def get_sequence_sources(self, context):
+def get_frame_sources(self, context):
-    items = [("-1", "None (1 frame)", "")]
+    items = [("-1", "First Frame (1 frame)", "")]
     orig_shape = tuple(self.orig_shape)
     if self.frame_count > 1:
-        items.append(("0", f"Frame ({self.frame_count} frames)", ""))
+        items.append(("0", f"Frames ({self.frame_count} frames)", ""))
     elif self.frame_count == 1 and self.channel_count > 1:
-        items.append(("4", f"Channel ({self.channel_count} frames)", ""))
+        items.append(("4", f"Channels ({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(("1", f"X-axis ({orig_shape[0]} frames)", ""))
-        items.append(("2", f"Y ({orig_shape[1]} frames)", ""))
+        items.append(("2", f"Y-axis ({orig_shape[1]} frames)", ""))
-        items.append(("3", f"Z ({orig_shape[2]} frames)", ""))
+        items.append(("3", f"Z-axis ({orig_shape[2]} frames)", ""))
 
     return items
 
@@ -424,10 +502,16 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
 
     channel_count: bpy.props.IntProperty()  # type: ignore
 
+    label_count: bpy.props.IntProperty()  # type: ignore
+
+    smooth: bpy.props.IntProperty(name="Smooth Size (Larger takes longer time)",
+                                  default=0)  # type: ignore
+
     read_as: bpy.props.EnumProperty(name="Read as",
-                                    default="scalar",
+                                    default="SCALAR",
-                                    items=[("scalar", "Scalar", ""),
+                                    items=[("SCALAR", "Scalar", ""),
-                                           ("label", "Labels", "")])  # type: ignore
+                                           ("LABEL", "Label", ""),
+                                           ("COLOR", "Color", "")])  # type: ignore
 
     bioxel_size: bpy.props.FloatProperty(name="Bioxel Size (Larger size means small resolution)",
                                          soft_min=0.1, soft_max=10.0,
@@ -445,11 +529,14 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
                                          min=1e-6, max=1e6,
                                          default=0.01)  # type: ignore
 
-    split_channels: bpy.props.BoolProperty(name="Split Channels",
+    remap: bpy.props.BoolProperty(name="Remap to 0~1",
                                   default=False)  # type: ignore
 
-    sequence_source: bpy.props.EnumProperty(name="Time Sequence From",
+    split_channel: bpy.props.BoolProperty(name="Split Channels",
-                                            items=get_sequence_sources)  # type: ignore
+                                          default=False)  # type: ignore
+
+    frame_source: bpy.props.EnumProperty(name="Frame From",
+                                         items=get_frame_sources)  # type: ignore
 
     def execute(self, context):
         def import_volumetric_data_func(self, context, cancel):
@@ -479,26 +566,26 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
 
             mat_scale = transforms3d.zooms.zfdir2aff(self.bioxel_size)
             affine = np.dot(meta['affine'], mat_scale)
-            kind = self.read_as
+            kind = self.read_as.lower()
 
             if cancel():
                 return
 
             # change shape as sequence or not
-            if self.sequence_source == "-1":
+            if self.frame_source == "-1":
                 data = data[0:1, :, :, :, :]
-            elif self.sequence_source == "0":
+            elif self.frame_source == "0":
                 # frame as frame
                 pass
-            elif self.sequence_source == "1":
+            elif self.frame_source == "1":
                 # X as frame
                 data = data.transpose(1, 0, 2, 3, 4)
                 shape = (1, shape[1], shape[2])
-            elif self.sequence_source == "2":
+            elif self.frame_source == "2":
                 # Y as frame
                 data = data.transpose(2, 1, 0, 3, 4)
                 shape = (shape[0], 1, shape[2])
-            elif self.sequence_source == "3":
+            elif self.frame_source == "3":
                 # Z as frame
                 data = data.transpose(3, 1, 2, 0, 4)
                 shape = (shape[0], shape[1], 1)
@@ -514,6 +601,7 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
                     sub_progress = progress + frame * sub_progress_step
                     progress_update(context, sub_progress,
                                     f"Processing {layer_name} Frame {frame+1}...")
+                    print(f"Processing {layer_name} Frame {frame+1}...")
                 return progress_callback
 
             layers = []
@@ -535,15 +623,77 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
                     progress_callback = progress_callback_factory(name_i,
                                                                   progress,
                                                                   progress_step)
+                    label_data = data == np.full_like(data, i+1)
+                    # label_data = label_data.astype(np.float32)
                     try:
-                        layer = Layer(data=data == np.full_like(data, i+1),
+                        layer = Layer(data=label_data,
                                       name=name_i,
-                                      kind=kind,
+                                      kind=kind)
-                                      affine=affine)
+
+                        layer.resize(shape=shape,
+                                     smooth=self.smooth,
+                                     progress_callback=progress_callback)
+
+                        layer.affine = affine
+
+                        layers.append(layer)
+                    except CancelledByUser:
+                        return
+                    except Exception as e:
+                        self.has_error = e
+                        return
+
+            if kind == "color":
+                if np.issubdtype(np.uint8, data.dtype):
+                    data = np.multiply(data, 1.0 / 256,
+                                       dtype=np.float32)
+                elif data.dtype.kind in ['u', 'i']:
+                    # Convert the normalized array to float dtype
+                    data = data.astype(np.float32)
+
+                    min_val = data.min()
+                    max_val = data.max()
+                    # Avoid division by zero if all values are the same
+                    if max_val != min_val:
+                        # Normalize the array to the range (0,1)
+                        data = (data - min_val) / (max_val - min_val)
+                    else:
+                        # If all values are the same, the normalized array will be all zeros
+                        data = np.zeros_like(data, dtype=np.float32)
+
+                else:
+                    data = data.astype(np.float32)
+
+                name = self.layer_name or "Color"
+                if data.shape[4] == 1:
+                    data = np.repeat(data, repeats=3, axis=4)
+                elif data.shape[4] == 2:
+                    d_shape = list(data.shape)
+                    d_shape = d_shape[:4] + [1]
+                    zore = np.zeros(tuple(d_shape), dtype=np.float32)
+                    data = np.concatenate((data, zore), axis=-1)
+                elif data.shape[4] > 3:
+                    data = data[:, :, :, :, :3]
+
+                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)
 
                     layer.resize(shape=shape,
                                  progress_callback=progress_callback)
 
+                    layer.affine = affine
+
                     layers.append(layer)
                 except CancelledByUser:
                     return
@@ -554,7 +704,21 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
             elif kind == "scalar":
                 name = self.layer_name or "Scalar"
 
-                if self.split_channels:
+                if self.remap:
+                    # Convert the normalized array to float dtype
+                    data = data.astype(np.float32)
+
+                    min_val = data.min()
+                    max_val = data.max()
+                    # Avoid division by zero if all values are the same
+                    if max_val != min_val:
+                        # Normalize the array to the range (0,1)
+                        data = (data - min_val) / (max_val - min_val)
+                    else:
+                        # If all values are the same, the normalized array will be all zeros
+                        data = np.zeros_like(data, dtype=np.float32)
+
+                if self.split_channel:
                     progress_step = 0.7/self.channel_count
 
                     for i in range(self.channel_count):
@@ -571,12 +735,13 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
                         try:
                             layer = Layer(data=data[:, :, :, :, i:i+1],
                                           name=name_i,
-                                          kind=kind,
+                                          kind=kind)
-                                          affine=affine)
 
                             layer.resize(shape=shape,
                                          progress_callback=progress_callback)
 
+                            layer.affine = affine
+
                             layers.append(layer)
                         except CancelledByUser:
                             return
@@ -596,12 +761,13 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
                     try:
                         layer = Layer(data=data,
                                       name=name,
-                                      kind=kind,
+                                      kind=kind)
-                                      affine=affine)
 
                         layer.resize(shape=shape,
                                      progress_callback=progress_callback)
 
+                        layer.affine = affine
+
                         layers.append(layer)
                     except CancelledByUser:
                         return
@@ -632,7 +798,7 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
     def modal(self, context, event):
         if event.type == 'ESC':
             self.is_cancelled = True
-            progress_update(context, 0, "Canceling...")
+            progress_update(context, 0.0, "Canceling...")
             return {'PASS_THROUGH'}
 
         if event.type != 'TIMER':
@@ -645,6 +811,7 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
         self.thread.join()
         context.window_manager.event_timer_remove(self._timer)
         bpy.types.STATUSBAR_HT_header.remove(progress_bar)
+        progress_update(context, 1.0)
 
         if self.is_cancelled:
             self.report({"WARNING"}, "Canncelled by user.")
@@ -668,20 +835,26 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
 
             container_obj = add_layers(self.layers,
                                        container_obj=container_obj,
-                                       cache_dir=get_cache_dir(context))
+                                       cache_dir=get_cache_dir())
         else:
-            container = Container(name=self.container_name,
+            name = self.container_name or "Container"
+            container = Container(name=name,
                                   layers=self.layers)
 
+            step_size = container.layers[0].bioxel_size[0]*10
             container_obj = container_to_obj(container,
                                              scene_scale=self.scene_scale,
-                                             cache_dir=get_cache_dir(context))
+                                             step_size=step_size,
+                                             cache_dir=get_cache_dir())
 
         select_object(container_obj)
 
         # Change render setting for better result
         if is_first_import:
-            change_render_setting(context)
+            bpy.ops.bioxelnodes.render_setting_preset('EXEC_DEFAULT',
+                                                      preset="balance")
+            bpy.context.scene.render.engine = 'CYCLES'
+            bpy.ops.bioxelnodes.slice_viewer('EXEC_DEFAULT')
 
         self.report({"INFO"}, "Successfully Imported")
         return {'FINISHED'}
@@ -704,55 +877,72 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
 
         # change shape as sequence or not
         channel_count = self.channel_count
-        if self.sequence_source == "-1":
+        frame_count = self.frame_count
+        if self.frame_source == "-1":
+            frame_count = 1
             pass
-        elif self.sequence_source == "0":
+        elif self.frame_source == "0":
             # frame as frame
             pass
-        elif self.sequence_source == "1":
+        elif self.frame_source == "1":
+            frame_count = orig_shape[0]
             layer_shape = (1, layer_shape[1], layer_shape[2])
-        elif self.sequence_source == "2":
+        elif self.frame_source == "2":
+            frame_count = orig_shape[1]
             layer_shape = (layer_shape[0], 1, layer_shape[2])
-        elif self.sequence_source == "3":
+        elif self.frame_source == "3":
+            frame_count = orig_shape[2]
             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"
+        if self.read_as == "SCALAR":
+            layer_count = channel_count if self.split_channel else 1
+            channel_count = 1
+        elif self.read_as == "LABEL":
+            layer_count = self.label_count
+            channel_count = 1
+        else:
+            layer_count = 1
+            channel_count = 3
 
         bioxel_count = layer_shape[0] * layer_shape[1] * layer_shape[2]
-        layer_shape_text = f"Shape from {str(orig_shape)} to {str(layer_shape)}"
+        orig_shape_text = f"[{self.frame_count}, ({orig_shape[0]},{orig_shape[1]},{orig_shape[2]}), {self.channel_count}]"
+        layer_shape_text = f"{layer_count} x [{frame_count}, ({layer_shape[0]},{layer_shape[1]},{layer_shape[2]}), {channel_count}]"
+
         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"
+
+        layout = self.layout
+        if self.container_obj_name == "":
             panel = layout.box()
+            panel.prop(self, "container_name")
             panel.prop(self, "scene_scale")
             panel.label(text=layer_size_text)
 
+        panel = layout.box()
+        panel.prop(self, "layer_name")
+        panel.prop(self, "bioxel_size")
+        row = panel.row()
+        row.prop(self, "orig_spacing")
+        panel.prop(self, "frame_source")
+
+        if self.read_as == "SCALAR":
+            panel.prop(self, "split_channel",
+                       text=f"Split Channel as Multi Layer")
+        elif self.read_as == "LABEL":
+            panel.prop(self, "smooth")
+
+        panel.label(
+            text="Dimension Order: [Frame, (X-axis,Y-axis,Z-axis), Channel]")
+        panel.label(
+            text=f"Shape from {orig_shape_text} to {layer_shape_text}")
+
 
 class ExportVolumetricData(bpy.types.Operator):
     bl_idname = "bioxelnodes.export_volumetric_data"

bioxelnodes/operators/layer.py

@@ -4,20 +4,15 @@ import bpy
 import numpy as np
 
 
+from ..exceptions import NoContent
 from ..bioxel.layer import Layer
-from ..bioxelutils.node import get_nodes_by_type
+from ..bioxelutils.node import add_node_to_graph
-from ..bioxelutils.container import add_layers, get_container_obj
+from ..bioxelutils.common import (get_container_obj, get_layer_kind, get_layer_label, get_layer_name,
-from ..bioxelutils.layer import obj_to_layer, get_container_layer_objs, get_layer_obj
+                                  get_layer_prop_value,
-from .utils import get_preferences, select_object
+                                  get_container_layer_objs,
-
+                                  get_node_type, is_missing_layer, move_node_to_node, set_layer_prop_value)
-
+from ..bioxelutils.layer import layer_to_obj, obj_to_layer
-def get_layer_prop_value(layer_obj: bpy.types.Object, prop: str):
+from ..utils import get_cache_dir, copy_to_dir, get_use_link
-    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):
@@ -25,86 +20,342 @@ def get_label_layer_selection(self, context):
     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":
+        kind = get_layer_prop_value(layer_obj, "kind")
+        name = get_layer_prop_value(layer_obj, "name")
+        if kind == "label":
             items.append((layer_obj.name,
-                          layer_obj.name,
+                          name,
                           ""))
 
     return items
 
 
-class LayerOperator():
+class FetchLayer(bpy.types.Operator):
+    bl_idname = "bioxelnodes.fetch_layer"
+    bl_label = "Fetch Layer"
+    bl_description = "Fetch layer from current container"
+    bl_icon = "NODE"
     bl_options = {'UNDO'}
-    base_obj: bpy.types.Object = None
 
-    def add_layer(self, context, layer):
+    layer_obj_name: bpy.props.StringProperty(
-        preferences = get_preferences(context)
+        options={"HIDDEN"})  # type: ignore
-        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):
+    def description(cls, context, properties):
-        label_objs = [obj for obj in context.selected_ids
+        layer_obj_name = properties.layer_obj_name
-                      if get_layer_prop_value(obj, "kind") == "scalar"]
+        layer_obj = bpy.data.objects.get(layer_obj_name)
-        return True if len(label_objs) > 0 else False
+        return "\n".join([f"{prop}: {get_layer_prop_value(layer_obj, prop)}"
+                          for prop in ["kind",
+                                       "bioxel_size",
+                                       "shape",
+                                       "frame_count",
+                                       "channel_count",
+                                       "min", "max"]])
 
-
+    @property
-class LabelOperator(LayerOperator):
+    def layer_obj(self):
-    @classmethod
+        return bpy.data.objects.get(self.layer_obj_name)
-    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)
+        if self.layer_obj == None:
+            self.report({"WARNING"}, "Get no layer.")
+            return {'FINISHED'}
 
-        modified_layer = base_layer.copy()
+        if is_missing_layer(self.layer_obj):
-        modified_layer.data = -base_layer.data
+            self.report({"WARNING"}, "Selected layer is lost.")
-        modified_layer.name = f"{base_layer.name}_Signed"
+            return {'FINISHED'}
 
-        self.add_layer(context, modified_layer)
+        bpy.ops.bioxelnodes.add_node('EXEC_DEFAULT',
+                                     node_name="FetchLayer",
+                                     node_label="Fetch Layer")
+        node = bpy.context.active_node
+
+        node.inputs[0].default_value = self.layer_obj
+        node.label = get_layer_label(self.layer_obj)
+
+        return {"FINISHED"}
+
+
+def get_selected_layers(context, layer_filter=None):
+    def _layer_filter(layer_obj, context):
+        return True
+
+    layer_filter = layer_filter or _layer_filter
+    select_objs = []
+    # node_group = context.space_data.edit_tree
+    for node in context.selected_nodes:
+        if get_node_type(node) == "BioxelNodes_FetchLayer":
+            layer_obj = node.inputs[0].default_value
+            if layer_obj is not None:
+                if layer_filter(layer_obj, context):
+                    select_objs.append(layer_obj)
+
+    return list(set(select_objs))
+
+
+def get_selected_layer(context, layer_filter=None):
+    layer_objs = get_selected_layers(context, layer_filter)
+    return layer_objs[0] if len(layer_objs) > 0 else None
+
+
+class OutputLayerOperator():
+    new_layer_name: bpy.props.StringProperty(name="New Name",
+                                             options={"SKIP_SAVE"})  # type: ignore
+
+    def operate(self, orig_layer: Layer, context):
+        """do the operation"""
+        return orig_layer
+
+    def add_layer_node(self, context, layer):
+        orig_node = context.selected_nodes[0]
+        layer_obj = layer_to_obj(layer,
+                                 container_obj=context.object,
+                                 cache_dir=get_cache_dir())
+        node_group = context.space_data.edit_tree
+        fetch_node = add_node_to_graph("FetchLayer",
+                                       node_group,
+                                       use_link=get_use_link())
+        fetch_node.label = get_layer_prop_value(layer_obj, "name")
+        fetch_node.inputs[0].default_value = layer_obj
+        move_node_to_node(fetch_node, orig_node, (0, -100))
+
+    def execute(self, context):
+        layer_obj = get_selected_layer(context)
+        if layer_obj == None:
+            self.report({"WARNING"}, "Get no layer.")
+            return {'FINISHED'}
+
+        if is_missing_layer(layer_obj):
+            self.report({"WARNING"}, "Selected layer is lost.")
+            return {'FINISHED'}
+
+        orig_layer = obj_to_layer(layer_obj)
+        try:
+            new_layer = self.operate(orig_layer, context)
+        except NoContent as e:
+            self.report({"WARNING"}, e.message)
+            return {'FINISHED'}
+
+        self.add_layer_node(context, new_layer)
         return {'FINISHED'}
 
 
-class FillOperator(ScalarOperator):
+class LayerOperator():
+
+    def operate(self, layer_obj: bpy.types.Object, context):
+        """do the operation"""
+        ...
+
+    def execute(self, context):
+        layer_obj = get_selected_layer(context)
+        if layer_obj == None:
+            self.report({"WARNING"}, "Get no layer.")
+            return {'FINISHED'}
+
+        if is_missing_layer(layer_obj):
+            self.report({"WARNING"}, "Selected layer is lost.")
+            return {'FINISHED'}
+
+        self.operate(layer_obj, context)
+
+        return {'FINISHED'}
+
+
+class RetimeLayer(bpy.types.Operator, LayerOperator):
+    bl_idname = "bioxelnodes.retime_layer"
+    bl_label = "Retime Sequence"
+    bl_description = "Retime layer time sequence"
+    bl_icon = "TIME"
+
+    frame_duration: bpy.props.IntProperty(name="Frames")  # type: ignore
+    frame_start: bpy.props.IntProperty(name="Start")  # type: ignore
+    frame_offset: bpy.props.IntProperty(name="Offset")  # type: ignore
+    sequence_mode: bpy.props.EnumProperty(name="Mode",
+                                          default="REPEAT",
+                                          items=[("CLIP", "Clip", ""),
+                                                 ("EXTEND", "Extend", ""),
+                                                 ("REPEAT", "Repeat", ""),
+                                                 ("PING_PONG", "Ping-Pong", "")])  # type: ignore
+
+    def operate(self, layer_obj, context):
+        layer_obj.data.frame_duration = self.frame_duration
+        layer_obj.data.frame_start = self.frame_start
+        layer_obj.data.frame_offset = self.frame_offset
+        layer_obj.data.sequence_mode = self.sequence_mode
+
     def invoke(self, context, event):
-        self.base_obj = get_layer_obj(bpy.context.active_object)
+        layer_obj = get_selected_layer(context)
-        scalar_min = get_layer_prop_value(self.base_obj, "min")
+        if layer_obj:
-        self.fill_value = min(scalar_min, 0)
+            self.frame_duration = layer_obj.data.frame_duration
-        context.window_manager.invoke_props_dialog(self, width=400)
+            self.frame_start = layer_obj.data.frame_start
+            self.frame_offset = layer_obj.data.frame_offset
+            self.sequence_mode = layer_obj.data.sequence_mode
+            name = get_layer_label(layer_obj)
+            context.window_manager.invoke_props_dialog(self,
+                                                       title=f"Retime {name}")
             return {'RUNNING_MODAL'}
+        else:
+            return self.execute(context)
 
 
-class FillByThreshold(bpy.types.Operator, FillOperator):
+class RelocateLayer(bpy.types.Operator):
-    bl_idname = "bioxelnodes.fill_by_threshold"
+    bl_idname = "bioxelnodes.relocate_layer"
-    bl_label = "Fill Value by Threshold"
+    bl_label = "Relocate Layer Cache"
-    bl_description = "Fill Value by Threshold"
+    bl_description = "Relocate layer cache"
+    bl_icon = "FILE"
 
-    threshold: bpy.props.FloatProperty(
+    filepath: bpy.props.StringProperty(subtype="FILE_PATH")  # type: ignore
-        name="Threshold",
+
-        soft_min=0, soft_max=1024,
+    def execute(self, context):
-        default=128,
+        layer_obj = get_selected_layer(context)
+        if layer_obj == None:
+            self.report({"WARNING"}, "Get no layer.")
+            return {'FINISHED'}
+
+        self.operate(layer_obj, context)
+
+        return {'FINISHED'}
+
+    def operate(self, layer_obj, context):
+        layer_obj.data.filepath = self.filepath
+
+    def invoke(self, context, event):
+        layer_obj = get_selected_layer(context)
+        if layer_obj:
+            context.window_manager.fileselect_add(self)
+            return {'RUNNING_MODAL'}
+        else:
+            return self.execute(context)
+
+
+class RenameLayer(bpy.types.Operator, LayerOperator):
+    bl_idname = "bioxelnodes.rename_layer"
+    bl_label = "Rename Layer"
+    bl_description = "Rename layer"
+    bl_icon = "FILE_FONT"
+
+    new_name: bpy.props.StringProperty(name="New Name",
+                                       options={"SKIP_SAVE"})  # type: ignore
+
+    def operate(self, layer_obj, context):
+        name = f"{layer_obj.parent.name}_{self.new_name}"
+        layer_obj.name = name
+        layer_obj.data.name = name
+
+        set_layer_prop_value(layer_obj, "name", self.new_name)
+
+        node_group = context.space_data.edit_tree
+        for node in node_group.nodes:
+            if get_node_type(node) == "BioxelNodes_FetchLayer":
+                if node.inputs[0].default_value == layer_obj:
+                    node.label = self.new_name
+
+    def invoke(self, context, event):
+        layer_obj = get_selected_layer(context)
+        if layer_obj:
+            self.new_name = get_layer_name(layer_obj)
+            name = get_layer_label(layer_obj)
+            context.window_manager.invoke_props_dialog(self,
+                                                       title=f"Rename {name}")
+            return {'RUNNING_MODAL'}
+        else:
+            return self.execute(context)
+
+
+class ResampleLayer(bpy.types.Operator, OutputLayerOperator):
+    bl_idname = "bioxelnodes.resample_layer"
+    bl_label = "Resample Value"
+    bl_description = "Resample value"
+    bl_icon = "ALIASED"
+
+    smooth: bpy.props.IntProperty(name="Smooth Size",
+                                  default=0,
+                                  soft_min=0, soft_max=5,
+                                  options={"SKIP_SAVE"})  # type: ignore
+
+    bioxel_size: bpy.props.FloatProperty(
+        name="Bioxel Size",
+        soft_min=0.1, soft_max=10.0,
+        default=1,
     )  # type: ignore
 
+    @staticmethod
+    def get_new_shape(orig_shape, orig_size, new_size):
+        return (int(orig_shape[0]*orig_size/new_size),
+                int(orig_shape[1]*orig_size/new_size),
+                int(orig_shape[2]*orig_size/new_size))
+
+    def operate(self, orig_layer: Layer, context):
+        new_layer = orig_layer.copy()
+        new_shape = self.get_new_shape(new_layer.shape,
+                                       new_layer.bioxel_size[0],
+                                       self.bioxel_size)
+
+        new_layer.resize(new_shape, self.smooth)
+        new_layer.name = self.new_layer_name \
+            or f"{orig_layer.name}_R-{self.bioxel_size:.2f}"
+        return new_layer
+
+    def draw(self, context):
+        layer_obj = get_selected_layer(context)
+        orig_shape = get_layer_prop_value(layer_obj, "shape")
+        orig_size = get_layer_prop_value(layer_obj, "bioxel_size")
+        new_shape = self.get_new_shape(orig_shape,
+                                       orig_size,
+                                       self.bioxel_size)
+
+        orig_shape = tuple(orig_shape)
+        bioxel_count = new_shape[0] * new_shape[1] * new_shape[2]
+
+        layer_shape_text = f"Shape from {str(orig_shape)} to {str(new_shape)}"
+        if bioxel_count > 100000000:
+            layer_shape_text += "**TOO LARGE!**"
+
+        layout = self.layout
+        layout.prop(self, "new_layer_name")
+        layout.prop(self, "bioxel_size")
+        layout.prop(self, "smooth")
+        layout.label(text=layer_shape_text)
+
+    def invoke(self, context, event):
+        layer_obj = get_selected_layer(context)
+        if layer_obj:
+            name = get_layer_label(layer_obj)
+            self.bioxel_size = get_layer_prop_value(layer_obj,
+                                                    "bioxel_size")
+            context.window_manager.invoke_props_dialog(self,
+                                                       title=f"Resample {name}")
+            return {'RUNNING_MODAL'}
+        else:
+            return self.execute(context)
+
+
+class SignScalar(bpy.types.Operator, OutputLayerOperator):
+    bl_idname = "bioxelnodes.sign_scalar"
+    bl_label = "Sign Value"
+    bl_description = "Sign value"
+    bl_icon = "REMOVE"
+
+    def operate(self, orig_layer: Layer, context):
+        new_layer = orig_layer.copy()
+        new_layer.data = -orig_layer.data
+        new_layer.name = self.new_layer_name \
+            or f"{orig_layer.name}_Sign"
+        return new_layer
+
+    def invoke(self, context, event):
+        layer_obj = get_selected_layer(context)
+        if layer_obj:
+            name = get_layer_label(layer_obj)
+            context.window_manager.invoke_props_dialog(self,
+                                                       title=f"Sign {name}")
+            return {'RUNNING_MODAL'}
+        else:
+            return self.execute(context)
+
+
+class FillOperator(OutputLayerOperator):
+
     fill_value: bpy.props.FloatProperty(
         name="Fill Value",
         soft_min=0, soft_max=1024.0,
@@ -112,30 +363,50 @@ class FillByThreshold(bpy.types.Operator, FillOperator):
     )  # type: ignore
 
     invert: bpy.props.BoolProperty(
-        name="Invert Area",
+        name="Invert Aera",
         default=True,
     )  # type: ignore
 
-    def execute(self, context):
+    def invoke(self, context, event):
-        base_layer = obj_to_layer(self.base_obj)
+        layer_obj = get_selected_layer(context)
+        if layer_obj:
+            name = get_layer_label(layer_obj)
+            context.window_manager.invoke_props_dialog(self,
+                                                       title=f"Fill {name}")
+            return {'RUNNING_MODAL'}
+        else:
+            return self.execute(context)
 
-        data = np.amax(base_layer.data, -1)
+
+class FillByThreshold(bpy.types.Operator, FillOperator):
+    bl_idname = "bioxelnodes.fill_by_threshold"
+    bl_label = "Fill Value by Threshold"
+    bl_description = "Fill value by threshold"
+    bl_icon = "EMPTY_SINGLE_ARROW"
+
+    threshold: bpy.props.FloatProperty(
+        name="Threshold",
+        soft_min=0, soft_max=1024,
+        default=128,
+    )  # type: ignore
+
+    def operate(self, orig_layer: Layer, context):
+        data = np.amax(orig_layer.data, -1)
         mask = data <= self.threshold \
             if self.invert else data > self.threshold
 
-        modified_layer = base_layer.copy()
+        new_layer = orig_layer.copy()
-        modified_layer.fill(self.fill_value, mask)
+        new_layer.fill(self.fill_value, mask, 0)
-        modified_layer.name = f"{base_layer.name}_{self.threshold}-Filled"
+        new_layer.name = self.new_layer_name \
-
+            or f"{orig_layer.name}_F-{self.threshold:.2f}"
-        self.add_layer(context, modified_layer)
+        return new_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"
+    bl_description = "Fill value by range"
+    bl_icon = "IPO_CONSTANT"
 
     from_min: bpy.props.FloatProperty(
         name="From Min",
@@ -149,103 +420,200 @@ class FillByRange(bpy.types.Operator, FillOperator):
         default=256,
     )  # type: ignore
 
-    fill_value: bpy.props.FloatProperty(
+    def operate(self, orig_layer: Layer, context):
-        name="Fill Value",
+        data = np.amax(orig_layer.data, -1)
-        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()
+        new_layer = orig_layer.copy()
-        modified_layer.fill(self.fill_value, mask)
+        new_layer.fill(self.fill_value, mask, 0)
-        modified_layer.name = f"{base_layer.name}_{self.from_min}-{self.from_max}-Filled"
+        new_layer.name = self.new_layer_name \
-
+            or f"{orig_layer.name}_F-{self.from_min:.2f}-{self.from_max:.2f}"
-        self.add_layer(context, modified_layer)
+        return new_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"
+    bl_description = "Fill value by label"
+    bl_icon = "MESH_CAPSULE"
 
-    label_obj_name: bpy.props.EnumProperty(
+    smooth: bpy.props.IntProperty(name="Smooth Size",
-        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
+                                  soft_min=0, soft_max=5,
+                                  options={"SKIP_SAVE"})  # type: ignore
 
-    invert: bpy.props.BoolProperty(
+    label_obj_name: bpy.props.EnumProperty(name="Label Layer",
-        name="Invert Label",
+                                           items=get_label_layer_selection)  # type: ignore
-        default=True,
-    )  # type: ignore
 
-    def execute(self, context):
+    def operate(self, orig_layer: Layer, context):
         label_obj = bpy.data.objects.get(self.label_obj_name)
-        if not label_obj:
+        if label_obj is None:
-            self.report({"WARNING"}, "Cannot find any label layer.")
+            raise NoContent("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)
+        label_layer.resize(orig_layer.shape, self.smooth)
         mask = np.amax(label_layer.data, -1)
         if self.invert:
             mask = 1 - mask
 
-        modified_layer = base_layer.copy()
+        new_layer = orig_layer.copy()
-        modified_layer.fill(self.fill_value, mask)
+        new_layer.fill(self.fill_value, mask, 0)
-        modified_layer.name = f"{base_layer.name}_{label_layer.name}-Filled"
+        new_layer.name = self.new_layer_name \
-
+            or f"{orig_layer.name}_F-{label_layer.name}"
-        self.add_layer(context, modified_layer)
+        return new_layer
-        return {'FINISHED'}
 
 
-class CombineLabels(bpy.types.Operator, LabelOperator):
+class CombineLabels(bpy.types.Operator, OutputLayerOperator):
     bl_idname = "bioxelnodes.combine_labels"
     bl_label = "Combine Labels"
     bl_description = "Combine all selected labels"
+    bl_icon = "MOD_BUILD"
 
     def execute(self, context):
-        label_objs = [obj for obj in context.selected_ids
+        def layer_filter(layer_obj, context):
-                      if get_layer_prop_value(obj, "kind") == "label"]
+            return get_layer_kind(layer_obj) == "label"
+
+        label_objs = get_selected_layers(context, layer_filter)
 
         if len(label_objs) < 2:
             self.report({"WARNING"}, "Not enough layers.")
             return {'FINISHED'}
+
         base_obj = label_objs[0]
         label_objs = label_objs[1:]
-        container_obj = base_obj.parent
 
         base_layer = obj_to_layer(base_obj)
-        modified_layer = base_layer.copy()
+        new_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(base_layer.data, label_layer.data)
+            new_layer.data = np.maximum(
+                new_layer.data, label_layer.data)
             label_names.append(label_layer.name)
 
-        modified_layer.name = f"{'-'.join(label_names)}-Combined"
+        new_layer.name = self.new_layer_name \
+            or f"C-{'-'.join(label_names)}"
 
-        self.add_layer(context, modified_layer)
+        self.add_layer_node(context, new_layer)
+        return {'FINISHED'}
+
+
+class BatchLayerOperator():
+    success_msg = "Successfully done selected layers."
+    fail_msg = "fails."
+
+    def execute(self, context):
+        layer_objs = self.get_layers(context)
+
+        fails = []
+        for layer_obj in layer_objs:
+            try:
+                self.operate(layer_obj, context)
+            except:
+                fails.append(layer_obj)
+
+        if len(fails) == 0:
+            self.report({"INFO"}, self.success_msg)
+        else:
+            self.report(
+                {"WARNING"}, f"{','.join([layer_obj.name for layer_obj in fails])} {self.fail_msg}")
 
         return {'FINISHED'}
+
+
+class SaveLayersCache(BatchLayerOperator):
+    fail_msg = "fail to save."
+
+    cache_dir: bpy.props.StringProperty(
+        name="Cache Directory",
+        subtype='DIR_PATH',
+        default="//"
+    )  # type: ignore
+
+    def operate(self, layer_obj, context):
+        output_dir = bpy.path.abspath(self.cache_dir)
+        source_dir = bpy.path.abspath(layer_obj.data.filepath)
+
+        source_path: Path = Path(source_dir).resolve()
+        is_sequence = layer_obj.data.is_sequence
+
+        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))
+
+        return {'FINISHED'}
+
+    def invoke(self, context, event):
+        context.window_manager.invoke_props_dialog(self)
+        return {'RUNNING_MODAL'}
+
+
+class RemoveLayers(BatchLayerOperator):
+    fail_msg = "fail to remove."
+
+    def operate(self, layer_obj, context):
+        for node_group in bpy.data.node_groups:
+            for node in node_group.nodes:
+                if get_node_type(node) == "BioxelNodes_FetchLayer":
+                    if node.inputs[0].default_value == layer_obj:
+                        node_group.nodes.remove(node)
+
+        cache_filepath = Path(bpy.path.abspath(
+            layer_obj.data.filepath)).resolve()
+
+        if cache_filepath.is_file():
+            if layer_obj.data.is_sequence:
+                for f in cache_filepath.parent.iterdir():
+                    f.unlink(missing_ok=True)
+            else:
+                cache_filepath.unlink(missing_ok=True)
+
+        # also remove layer object
+        bpy.data.volumes.remove(layer_obj.data)
+
+        return {'FINISHED'}
+
+    def invoke(self, context, event):
+        context.window_manager.invoke_confirm(self,
+                                              event,
+                                              message=f"Are you sure to remove them?")
+        return {'RUNNING_MODAL'}
+
+
+class SaveSelectedLayersCache(bpy.types.Operator, SaveLayersCache):
+    bl_idname = "bioxelnodes.save_selected_layers_cache"
+    bl_label = "Save Selected Layers Cache"
+    bl_description = "Save selected layers' Cache"
+    bl_icon = "FILE_TICK"
+
+    success_msg = "Successfully saved all selected layers."
+
+    def get_layers(self, context):
+        def is_not_missing(layer_obj, context):
+            return not is_missing_layer(layer_obj)
+        return get_selected_layers(context, is_not_missing)
+
+
+class RemoveSelectedLayers(bpy.types.Operator, RemoveLayers):
+    bl_idname = "bioxelnodes.remove_selected_layers"
+    bl_label = "Remove Selected Layers"
+    bl_description = "Remove selected layers"
+    bl_icon = "TRASH"
+
+    success_msg = "Successfully removed all selected layers."
+
+    def get_layers(self, context):
+        return get_selected_layers(context)

bioxelnodes/operators/misc.py

@@ -1,81 +1,54 @@
-import re
+import webbrowser
 import bpy
 from pathlib import Path
 import shutil
 
+from ..bioxelutils.common import get_all_layer_objs, get_node_lib_path, get_node_version, is_missing_layer, set_file_prop
+from .layer import RemoveLayers, SaveLayersCache
 
-from ..utils import copy_to_dir
+from ..constants import LATEST_NODE_LIB_PATH, VERSIONS
-from .utils import get_cache_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"
 
 
-class ReLinkNodes(bpy.types.Operator):
+class ReLinkNodeLib(bpy.types.Operator):
-    bl_idname = "bioxelnodes.relink_nodes"
+    bl_idname = "bioxelnodes.relink_node_lib"
-    bl_label = "Relink Nodes to Addon"
+    bl_label = "Relink Node Library"
-    bl_description = "Relink all nodes to addon source"
+    bl_description = "Relink all nodes to addon library source"
+    bl_options = {'UNDO'}
+
+    index: bpy.props.IntProperty()  # type: ignore
 
     def execute(self, context):
-        file_name = Path(custom_nodes.nodes_file).name
+        node_version = VERSIONS[self.index]['node_version']
-        for lib in bpy.data.libraries:
+        lib_path = get_node_lib_path(node_version) \
-            lib_path = Path(bpy.path.abspath(lib.filepath)).resolve()
+            if self.index != 0 else LATEST_NODE_LIB_PATH
-            lib_name = lib_path.name
+
-            if lib_name == file_name:
+        node_libs = []
-                if str(lib_path) != custom_nodes.nodes_file:
+        for node_group in bpy.data.node_groups:
-                    lib.filepath = custom_nodes.nodes_file
+            if node_group.name.startswith("BioxelNodes"):
+                node_lib = node_group.library
+                if node_lib:
+                    node_libs.append(node_lib)
+
+        node_libs = list(set(node_libs))
+
+        for node_lib in node_libs:
+            node_lib.filepath = str(lib_path)
+            # FIXME: may cause crash
+            node_lib.reload()
+
+        set_file_prop("node_version", node_version)
 
         self.report({"INFO"}, f"Successfully relinked.")
 
         return {'FINISHED'}
 
 
-def save_layer_cache(layer_obj, output_dir):
+class SaveNodeLib(bpy.types.Operator):
-    pattern = r'\.\d{4}\.'
+    bl_idname = "bioxelnodes.save_node_lib"
-
+    bl_label = "Save Node Library"
-    # "//"
+    bl_description = "Save node library file to local"
-    output_dir = bpy.path.abspath(output_dir)
+    bl_options = {'UNDO'}
-    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_cache: bpy.props.BoolProperty(
-        name="Save Layer Caches",
-        default=True,
-    )  # type: ignore
-
-    cache_dir: bpy.props.StringProperty(
-        name="Cache Directory",
-        subtype='DIR_PATH',
-        default="//"
-    )  # type: ignore
-
-    save_lib: bpy.props.BoolProperty(
-        name="Save Node Library File",
-        default=True,
-    )  # type: ignore
 
     lib_dir: bpy.props.StringProperty(
         name="Library Directory",
@@ -84,132 +57,220 @@ class SaveStagedData(bpy.types.Operator):
     )  # type: ignore
 
     def execute(self, context):
-        if self.save_lib:
+        node_version = get_node_version()
-            files = []
-            for classname in dir(bpy.types):
-                if CLASS_PREFIX in classname:
-                    cls = getattr(bpy.types, classname)
-                    files.append(cls.nodes_file)
-            files = list(set(files))
 
-            for file in files:
+        if node_version is None:
-                file_name = Path(file).name
+            node_version = VERSIONS[0]["node_version"]
-                # "//"
-                lib_dir = bpy.path.abspath(self.lib_dir)
-
-                output_path: Path = Path(lib_dir, file_name).resolve()
-                source_path: Path = Path(file).resolve()
-
-                if output_path != source_path:
-                    shutil.copy(source_path, output_path)
-
-                for lib in bpy.data.libraries:
-                    lib_path = Path(bpy.path.abspath(lib.filepath)).resolve()
-                    if lib_path == source_path:
-                        blend_path = Path(bpy.path.abspath("//")).resolve()
-                        lib.filepath = bpy.path.relpath(
-                            str(output_path), start=str(blend_path))
-
-                self.report({"INFO"}, f"Successfully saved to {output_path}")
-
-        if self.save_cache:
-            fails = []
-            for layer in get_all_layer_objs():
-                try:
-                    save_layer_cache(layer, self.cache_dir)
-                except:
-                    fails.append(layer)
-
-            if len(fails) == 0:
-                self.report({"INFO"}, f"Successfully saved bioxel layers.")
         else:
-                self.report(
+            if node_version not in [v["node_version"] for v in VERSIONS]:
-                    {"WARNING"}, f"{','.join([layer.name for layer in fails])} fail to save.")
+                node_version = VERSIONS[0]["node_version"]
+
+        if node_version == VERSIONS[0]["node_version"]:
+            lib_path = LATEST_NODE_LIB_PATH
+        else:
+            lib_path = get_node_lib_path(node_version)
+
+        version_str = "v"+".".join([str(i) for i in list(node_version)])
+
+        lib_dir = bpy.path.abspath(self.lib_dir)
+        local_lib_path: Path = Path(lib_dir,
+                                    f"BioxelNodes_{version_str}.blend").resolve()
+        node_lib_path: Path = lib_path
+        blend_path = Path(bpy.path.abspath("//")).resolve()
+
+        if local_lib_path != node_lib_path:
+            shutil.copy(node_lib_path, local_lib_path)
+
+        libs = []
+        for node_group in bpy.data.node_groups:
+            if node_group.name.startswith("BioxelNodes"):
+                if node_group.library:
+                    libs.append(node_group.library)
+
+        libs = list(set(libs))
+        for lib in libs:
+            lib.filepath = bpy.path.relpath(str(local_lib_path),
+                                            start=str(blend_path))
 
         return {'FINISHED'}
 
     def invoke(self, context, event):
-        context.window_manager.invoke_props_dialog(self,
+        context.window_manager.invoke_props_dialog(self)
-                                                   width=500)
         return {'RUNNING_MODAL'}
 
     @classmethod
     def poll(cls, context):
         return bpy.data.is_saved
 
-    def draw(self, context):
-        layout = self.layout
-        panel = layout.box()
-        panel.prop(self, "save_cache")
-        panel.prop(self, "cache_dir")
-        panel = layout.box()
-        panel.prop(self, "save_lib")
-        panel.prop(self, "lib_dir")
 
-
+class CleanTemp(bpy.types.Operator):
-class SaveCaches(bpy.types.Operator):
+    bl_idname = "bioxelnodes.clear_temp"
-    bl_idname = "bioxelnodes.save_caches"
+    bl_label = "Clean Temp"
-    bl_label = "Save Caches"
+    bl_description = "Clean all cache in temp (include other project cache)"
-    bl_description = "Save Container's caches to directory."
-
-    cache_dir: bpy.props.StringProperty(
-        name="Layer Directory",
-        subtype='DIR_PATH',
-        default="//"
-    )  # type: ignore
-
-    @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()
+        cache_dir = get_cache_dir()
-
-        if len(container_objs) == 0:
-            self.report({"WARNING"}, "Cannot find any bioxel container.")
-            return {'FINISHED'}
-
-        fails = []
-        for container_obj in container_objs:
-            for layer_obj in get_container_layer_objs(container_obj):
-                try:
-                    save_layer_cache(layer_obj, self.cache_dir)
-                except:
-                    fails.append(layer_obj)
-
-        if len(fails) == 0:
-            self.report({"INFO"}, f"Successfully saved bioxel layers.")
-        else:
-            self.report(
-                {"WARNING"}, f"{','.join([layer.name for layer in fails])} fail to save.")
-
-        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        context.window_manager.invoke_props_dialog(self,
-                                                   width=500)
-        return {'RUNNING_MODAL'}
-
-
-class CleanAllCaches(bpy.types.Operator):
-    bl_idname = "bioxelnodes.clear_all_caches"
-    bl_label = "Clean All Caches in Temp"
-    bl_description = "Clean all caches saved in temp"
-
-    def execute(self, context):
-        cache_dir = get_cache_dir(context)
         try:
             shutil.rmtree(cache_dir)
-            self.report({"INFO"}, f"Successfully cleaned caches.")
+            self.report({"INFO"}, f"Successfully cleaned temp.")
             return {'FINISHED'}
         except:
             self.report({"WARNING"},
-                        "Fail to clean caches, you may do it manually.")
+                        "Fail to clean temp, you may do it manually.")
             return {'CANCELLED'}
 
     def invoke(self, context, event):
         context.window_manager.invoke_confirm(self,
                                               event,
-                                              message="All caches will be cleaned, include other project files, do you still want to clean?")
+                                              message="All temp files will be removed, include other project cache, do you still want to clean?")
         return {'RUNNING_MODAL'}
+
+
+class RenderSettingPreset(bpy.types.Operator):
+    bl_idname = "bioxelnodes.render_setting_preset"
+    bl_label = "Render Setting Presets"
+    bl_description = "Render setting presets for bioxel"
+    bl_options = {'UNDO'}
+
+    PRESETS = {
+        "performance": "Performance",
+        "balance": "Balance",
+        "quality": "Quality",
+    }
+
+    preset: bpy.props.EnumProperty(name="Preset",
+                                   default="balance",
+                                   items=[(k, v, "")
+                                          for k, v in PRESETS.items()])  # type: ignore
+
+    def execute(self, context):
+        if self.preset == "performance":
+            # EEVEE
+            # bpy.context.scene.eevee.use_taa_reprojection = False
+            bpy.context.scene.eevee.volumetric_tile_size = '2'
+            bpy.context.scene.eevee.volumetric_shadow_samples = 32
+            bpy.context.scene.eevee.volumetric_samples = 64
+            bpy.context.scene.eevee.volumetric_ray_depth = 1
+            bpy.context.scene.eevee.use_volumetric_shadows = True
+
+            # Cycles
+            bpy.context.scene.cycles.shading_system = True
+            bpy.context.scene.cycles.volume_bounces = 0
+            bpy.context.scene.cycles.transparent_max_bounces = 4
+            bpy.context.scene.cycles.volume_preview_step_rate = 4
+            bpy.context.scene.cycles.volume_step_rate = 4
+
+        elif self.preset == "balance":
+            # EEVEE
+            # bpy.context.scene.eevee.use_taa_reprojection = False
+            bpy.context.scene.eevee.volumetric_tile_size = '2'
+            bpy.context.scene.eevee.volumetric_shadow_samples = 64
+            bpy.context.scene.eevee.volumetric_samples = 128
+            bpy.context.scene.eevee.volumetric_ray_depth = 8
+            bpy.context.scene.eevee.use_volumetric_shadows = True
+
+            # Cycles
+            bpy.context.scene.cycles.shading_system = True
+            bpy.context.scene.cycles.volume_bounces = 4
+            bpy.context.scene.cycles.transparent_max_bounces = 8
+            bpy.context.scene.cycles.volume_preview_step_rate = 1
+            bpy.context.scene.cycles.volume_step_rate = 1
+
+        elif self.preset == "quality":
+            # EEVEE
+            # 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.volumetric_ray_depth = 16
+            bpy.context.scene.eevee.use_volumetric_shadows = True
+
+            # Cycles
+            bpy.context.scene.cycles.shading_system = True
+            bpy.context.scene.cycles.volume_bounces = 8
+            bpy.context.scene.cycles.transparent_max_bounces = 16
+            bpy.context.scene.cycles.volume_preview_step_rate = 0.5
+            bpy.context.scene.cycles.volume_step_rate = 0.5
+
+        return {'FINISHED'}
+
+
+class SliceViewer(bpy.types.Operator):
+    bl_idname = "bioxelnodes.slice_viewer"
+    bl_label = "Slice Viewer"
+    bl_description = "A preview scene setting for viewing slicers"
+    bl_icon = "FILE_VOLUME"
+
+    def execute(self, context):
+        # 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 = 128
+        bpy.context.scene.eevee.volumetric_ray_depth = 1
+        bpy.context.scene.eevee.use_volumetric_shadows = False
+
+        for area in bpy.context.screen.areas:
+            if area.type == 'VIEW_3D':
+                area.spaces[0].shading.type = 'MATERIAL'
+                area.spaces[0].shading.studio_light = 'studio.exr'
+                area.spaces[0].shading.studiolight_intensity = 2.5
+                area.spaces[0].shading.use_scene_lights = False
+                area.spaces[0].shading.use_scene_world = False
+
+        return {'FINISHED'}
+
+
+def get_all_layers(layer_filter=None):
+    def _layer_filter(layer_obj):
+        return True
+
+    layer_filter = layer_filter or _layer_filter
+    layer_objs = get_all_layer_objs()
+    return [obj for obj in layer_objs if layer_filter(obj)]
+
+
+class SaveAllLayersCache(bpy.types.Operator, SaveLayersCache):
+    bl_idname = "bioxelnodes.save_all_layers_cache"
+    bl_label = "Save All Layers Cache"
+    bl_description = "Save all cache of this file"
+    bl_icon = "FILE_TICK"
+
+    success_msg = "Successfully saved all layers."
+
+    def get_layers(self, context):
+        def is_not_missing(layer_obj):
+            return not is_missing_layer(layer_obj)
+        return get_all_layers(is_not_missing)
+
+
+class RemoveAllMissingLayers(bpy.types.Operator, RemoveLayers):
+    bl_idname = "bioxelnodes.remove_all_missing_layers"
+    bl_label = "Remove All Missing Layers"
+    bl_description = "Remove all current container missing layers"
+    bl_icon = "BRUSH_DATA"
+
+    success_msg = "Successfully removed all missing layers."
+
+    def get_layers(self, context):
+        def is_missing(layer_obj):
+            return is_missing_layer(layer_obj)
+        return get_all_layers(is_missing)
+
+    def invoke(self, context, event):
+        context.window_manager.invoke_confirm(self,
+                                              event,
+                                              message=f"Are you sure to remove all **Missing** layers?")
+        return {'RUNNING_MODAL'}
+
+
+class Help(bpy.types.Operator):
+    bl_idname = "bioxelnodes.help"
+    bl_label = "Need Help?"
+    bl_description = "Online Manual for Beginner"
+    bl_icon = "HELP"
+
+    def execute(self, context):
+        webbrowser.open(
+            'https://omoolab.github.io/BioxelNodes/latest/', new=2)
+
+        return {'FINISHED'}

bioxelnodes/operators/node.py

@@ -0,0 +1,60 @@
+import bpy
+
+from ..bioxelutils.common import is_incompatible, local_lib_not_updated
+from ..bioxelutils.node import assign_node_tree, get_node_tree
+from ..utils import get_use_link
+
+
+class AddNode(bpy.types.Operator):
+    bl_idname = "bioxelnodes.add_node"
+    bl_label = "Add Node"
+    bl_options = {"REGISTER", "UNDO"}
+
+    node_name: bpy.props.StringProperty(
+        default='',
+    )  # type: ignore
+
+    node_label: bpy.props.StringProperty(
+        default=''
+    )  # type: ignore
+
+    node_description: bpy.props.StringProperty(
+        default="",
+    )  # type: ignore
+
+    @property
+    def node_type(self):
+        return f"BioxelNodes_{self.node_name}"
+
+    def execute(self, context):
+        space = context.space_data
+        if space.type != "NODE_EDITOR":
+            self.report({"ERROR"}, "Not in node editor.")
+            return {'CANCELLED'}
+
+        if not space.edit_tree.is_editable:
+            self.report({"ERROR"}, "Not editable.")
+            return {'CANCELLED'}
+
+        if is_incompatible():
+            self.report({"ERROR"},
+                        "Current addon verison is not compatible to this file. If you insist on editing this file please keep the same addon version.")
+            return {'CANCELLED'}
+
+        node_tree = get_node_tree(self.node_type, get_use_link())
+        bpy.ops.node.add_node(
+            'INVOKE_DEFAULT',
+            type='GeometryNodeGroup',
+            use_transform=True
+        )
+        node = bpy.context.active_node
+        assign_node_tree(node, node_tree)
+        node.label = self.node_label
+
+        node.show_options = False
+
+        if local_lib_not_updated():
+            self.report({"WARNING"},
+                        "Local node library version does not match the current addon version, which may cause problems, please save the node library again.")
+
+        return {"FINISHED"}

bioxelnodes/operators/utils.py

@@ -1,60 +0,0 @@
-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

@@ -1,6 +1,7 @@
 import bpy
 from pathlib import Path
 
+
 class BioxelNodesPreferences(bpy.types.AddonPreferences):
     bl_idname = __package__
 
@@ -10,14 +11,19 @@ class BioxelNodesPreferences(bpy.types.AddonPreferences):
         default=str(Path(Path.home(), '.bioxelnodes'))
     )  # type: ignore
 
-    do_change_render_setting: bpy.props.BoolProperty(
+    change_render_setting: bpy.props.BoolProperty(
-        name="Change Render Setting",
+        name="Change Render Setting on First Import",
         default=True,
     )  # type: ignore
 
+    node_import_method: bpy.props.EnumProperty(name="Node Import Method",
+                                               default="LINK",
+                                               items=[("LINK", "Link", ""),
+                                                      ("APPEND", "Append (Reuse Data)", "")])  # 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")
+        layout.prop(self, "change_render_setting")
+        layout.prop(self, "node_import_method")

bioxelnodes/props.py

@@ -1,5 +1,44 @@
 import bpy
 
+from .bioxelutils.common import get_node_type
+
+
+class BIOXELNODES_UL_layer_list(bpy.types.UIList):
+    def draw_item(self, context, layout, data, item, icon, active_data, active_propname):
+        layout.label(text=item.label, translate=False, icon_value=icon)
+
+
 class BIOXELNODES_Series(bpy.types.PropertyGroup):
     id: bpy.props.StringProperty()   # type: ignore
     label: bpy.props.StringProperty()   # type: ignore
+
+
+def select_layer(self, context):
+    layer_list_UL = bpy.context.window_manager.bioxelnodes_layer_list_UL
+    layer_list = layer_list_UL.layer_list
+    layer_list_active = layer_list_UL.layer_list_active
+
+    if len(layer_list) > 0 and layer_list_active != -1 and layer_list_active < len(layer_list):
+        layer_obj = bpy.data.objects[layer_list[layer_list_active].obj_name]
+        node_group = context.space_data.edit_tree
+        for node in node_group.nodes:
+            node.select = False
+            if get_node_type(node) == "BioxelNodes_FetchLayer":
+                if node.inputs[0].default_value == layer_obj:
+                    node.select = True
+
+    layer_list_UL.layer_list_active = -1
+
+
+class BIOXELNODES_Layer(bpy.types.PropertyGroup):
+    obj_name: bpy.props.StringProperty()   # type: ignore
+    label: bpy.props.StringProperty()   # type: ignore
+    info_text: bpy.props.StringProperty()   # type: ignore
+
+
+class BIOXELNODES_LayerListUL(bpy.types.PropertyGroup):
+    layer_list: bpy.props.CollectionProperty(
+        type=BIOXELNODES_Layer)  # type: ignore
+    layer_list_active: bpy.props.IntProperty(default=-1,
+                                             update=select_layer,
+                                             options=set())  # type: ignore

bioxelnodes/utils.py

@@ -1,5 +1,6 @@
 from pathlib import Path
 import shutil
+import bpy
 
 
 def copy_to_dir(source_path, dir_path, new_name=None, exist_ok=True):
@@ -30,3 +31,42 @@ def copy_to_dir(source_path, dir_path, new_name=None, exist_ok=True):
 
     if not target_path.exists():
         raise Exception
+
+
+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():
+    return bpy.context.preferences.addons[__package__].preferences
+
+
+def get_cache_dir():
+    preferences = get_preferences()
+    cache_path = Path(preferences.cache_dir, 'VDBs')
+    cache_path.mkdir(parents=True, exist_ok=True)
+    return str(cache_path)
+
+
+def get_use_link():
+    preferences = get_preferences()
+    return preferences.node_import_method == "LINK"

build.py

@@ -16,7 +16,8 @@ required_packages = ["SimpleITK==2.3.1",
                      "pyometiff==1.0.0",
                      "mrcfile==1.5.1",
                      "h5py==3.11.0",
-                     "transforms3d==0.4.2"]
+                     "transforms3d==0.4.2",
+                     "tifffile==2024.7.24"]
 
 
 platforms = {"windows-x64": Platform(pypi_suffix="win_amd64",

docs/SARS-Cov-2.md

@@ -0,0 +1,99 @@
+# SARS-Cov-2
+
+![alt text](assets/SARS-Cov-2/image.png)
+
+![alt text](assets/SARS-Cov-2/image-1.png)
+
+In this tutorial, we'll make a structural visualzation of the SARS-Cov-2 Virus. Please see [step by step](step_by_step.md) to make sure you have a basic understanding of how to use the addon, and make sure the addon version is v1.0.2 or higher!
+
+Research data is from paper published in September 2020 in Cell Press ([https://www.cell.com/cell/fulltext/S0092-8674(20)31159-4](<https://www.cell.com/cell/fulltext/S0092-8674(20)31159-4>)) by Li Sai team at Tsinghua University. This research revealed the molecular assembly of the authentic SARS-CoV-2 virus using cryoelectron tomography (cryo-ET) and subtomogram averaging (STA). Here is an official video of this study
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/JSKl5VY4k5w?si=t4LhrCRebxrX_Saf&amp;controls=0" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+"It remains enigmatic how coronaviruses pack the ∼30-kb RNA into the ∼80-nm-diameter viral lumen. Are the RNPs ordered relative to each other to avoid RNA entangling, knotting, or even damage or are they involved in virus assembly?" Three assembly classes were proposed in the paper, we will make a visualzation of the "eggs-in-a-nest"-shaped RNPs assembly, based on real cryo-ET data.
+
+## Download and import data
+
+The data of this research is hosted on EMDB ([https://www.ebi.ac.uk/emdb](https://www.ebi.ac.uk/emdb)), and the website of SARS-Cov-2 virus is [here](https://www.ebi.ac.uk/emdb/EMD-30430). Open the page, find "Download" button and select the first selection "3D Volume (.map.gz)".
+
+In case you can't download data, you can download here.
+
+[SARS-Cov-2.map](https://drive.google.com/file/d/1LMybsmTVbwQ38_eqAx6hbZTc5p2fdcjK/view?usp=sharing)
+
+After downloading, put it into any directory and import the data. In the import options, it is recommended to adjust the Bioxel Size to 5, in order to reduce the shape of the data to increase the speed of calculation and rendering. If you are confident in the performance of your hardware, you can leave the original 2.72 unchanged. After adjusting the Bioxel Size, the shape of the converted data will be calculated below based on the current bioxel size. The amount of data will increase exponentially with larger shape, and may result in OOM (out of memory).
+
+## Cutout the Virus
+
+After importing, you can get the virus by creating and connecting nodes and setting parameters as shown below
+
+![alt text](assets/SARS-Cov-2/image-2.png)
+
+Place the light and the camera in the way as below. The backlight is a area light, color white, intensity 500W, spread 90°, and inside the virus, place a point light, color `FFD08D`, intensity 5W. Camera focal length is 200 mm. the background color is pure black. The Look of the color management is High Contrast.
+
+![alt text](assets/SARS-Cov-2/image-3.png)
+
+Continue editing the node, followed by "Set Properies" and "Set Color by Ramp 4" node, the parameters of these two nodes are set as shown in the figure, where the color part, from top to bottom, is set to `E1D0FC` (1.0), `FFE42D` (0.5), `3793FF` (0.5), `FFFF8EC` (0.1) (alpha value in parentheses). Color alpha also affects density.
+
+![alt text](assets/SARS-Cov-2/image-4.png)
+
+If you feel that rendering is too slow, see [here](improve_performance.md) for suggestions
+
+## Color the RNPs alone
+
+The current rendering is pretty good, but considering that my goal is to make it clear how the RNPs are arranged within the virus, the RNPs should be colored differently than the others. So how to color the RNPs alone?
+
+First of all, we have to separate the RNPs. The value of RNPs is between the membrane and S protein, so it is very difficult to separate. The good thing is that the virus is spherical, we can separate the RNPs part of the virus from the rest by using a sphere cutter. To do so, in the Geometry Nodes panel menu of the container, click **Bioxel Nodes > Add a Cutter > Sphere Cutter**, and adjust the scale and position of the newly created sphere object named "Sphere_Cutter" appropriately, so that it can just separate the internal RNPs and membrane of the virus.
+
+![alt text](assets/SARS-Cov-2/image-5.png)
+
+The process of changing the position of the "Sphere_Cutter" object can be very laggy, then you can turn off "With Surface" and do it in Slice Viewer mode. Once you are happy with it, you can restore the settings.
+
+Then we turn on Invert in the "Sphere Cutter" node and you can see the opposite result. This way we've managed to separate the two, next let's color them separately and finally merge them with Join Component. Create and join the nodes as shown below, where the second Cutter node is copied and the color value in Set Color is `FFDDFE` (0.5). If all is well, the rendering should look like below.
+
+![alt text](assets/SARS-Cov-2/image-6.png)
+
+At this point, the rendering of a SARS-Cov-2 virus is complete!
+
+## Render RNPs and Membranes
+
+Realistic rendering is great, but Non-photorealistic rendering (NPR) is better for presenting structural information. So I will render ultrastructure of the RNPs assembly with toon shader.
+
+![alt text](assets/SARS-Cov-2/image-7.png)
+
+The silhouettes of RNPs uses Blender's Line Art feature, but Line Art must be based on a mesh. Select the nodes that are extruding the RNPs (i.e., the "Cut" nodes that are in charge of cutting out the RNPs), and right-click, click **Bioxel Nodes > Extract Mesh**. This gives you a new mesh object of the RNPs.
+
+Extract the membrane mesh in the same way.
+
+The membrane has a much higher value than the rest of the virus, so let's create a new "Cutout" node, also after the ReCenter, but with the threshold adjusted to 0.13. After the Cutout, connect to the "To Surface" node and parameterize it as shown in the figure, noting that the Remove Island Threshold is set to 1000 so that any fragments smaller than 1000 pts be eliminated. Then select the "To Surface" node, and perform the operation of extracting the mesh.
+
+![alt text](assets/SARS-Cov-2/image-8.png)
+
+The mesh of the membrane needs to be cut in half, this can be done with the Box Trim brush in sculpt mode or with the Boolean modifier. the mesh of the RNPs may also need some repair work, I cleaned up some of the broken surfaces of the RNPs. all the meshes are now ready to be used.
+
+![alt text](assets/SARS-Cov-2/image-9.png)
+
+For Line Art, please see the video tutorial from Blender Secrets.
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/aIWdBq7-ias?si=CrcStx5VVJBwDpzu&amp;controls=0" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+Finally, an infographic on the ultrastructure of RNPs is done!
+
+![alt text](assets/SARS-Cov-2/image-1.png)
+
+If you have trouble following the docs, you can download the project files.
+
+[SARS-Cov-2.zip](https://drive.google.com/file/d/15GpIoIjVAE-Jr98zWo7oupuk1KfRVPmk/view?usp=sharing)
+
+## Homework
+
+Other data relevant to the study are provided in the paper, you could try visualizing them.
+
+![alt text](assets/SARS-Cov-2/image-10.png)
+
+Go to the official EMDB website https://www.ebi.ac.uk/emdb/ and enter the EMD number in the search box to get them.
+
+The Electron Microscopy Data Bank (EMDB) is a public repository for cryogenic-sample Electron Microscopy (cryoEM) volumes and representative tomograms of macromolecular complexes and subcellular structures. If you want to get data on other virus, just enter their name in the search box. For example, hepatitis B virus, enter it into the search box, then select Virus in the Sample Type on the left side, and download the data you need (it is better to find the corresponding paper to clarify the data information).
+
+**Try to visualize hepatitis B virus.**
+
+![alt text](assets/SARS-Cov-2/image-11.png)

docs/advanced_usage.md

@@ -0,0 +1,118 @@
+# Advanced Usage
+
+## Concepts
+
+In the previous section, I mentioned some key concepts, I'll describe them in detail so that you can better understand the following operations.
+
+### Container
+
+First is the **Container**, it is the easiest to describe, you can think of it as a scene, or a solver container. it is the stage that carries all stuffs.
+
+### Layer
+
+Second is the **Layer**, which represents different fields of data under the same location in container of the same subject. Just as view layers in any map app, one as roads, one as satellite view, while in Bioxel, one as MRI, one as CT, one as electrical signals, etc. Some layers are for material, such as color, density, etc., we call them **Material Layer**. One container contains different layers of one subject each. Any external data imported into the container is converted into the layer.
+
+### Component
+
+Finally, the **Component**, which is a fragment of **Material Layer**. Multiple materials (Matters) may exist within the same area with different meanings of presentation, like objects in blender, each representing a part of the scene. Bioxel Nodes provides a series of nodes and tools that allow the user to create material layers (Components) based on the other layers (serve as source data), In the previous section, we used the CT data (layer) to make the material (matter) of skull, this process known as materialization.
+
+## Attache the Muscles to the Skull
+
+Multiple components can exist in one container, just as multiple objects can exist in one scene. They can be controlled individually or combined with each other to build complex scenes. Next, let's try cutouting muscle from the VHP anatomical images and attaching the muscles to the skull that created in the previous section. The anatomical images are very large, so I've cropped and scaled them down to 1/4 of their original size for ease of use. Download the file and unzip it into a new directory.
+
+[VHP_M_AnatomicalImages_Head.zip](https://drive.google.com/file/d/164AjQX0tmgUpWZlleJ5i1IKHco4ytDu2/view?usp=drive_link)
+
+You can also download the data directly from the official website, [https://data.lhncbc.nlm.nih.gov/public/Visible-Human/Male-Images/PNG_format/head/index.html](https://data.lhncbc.nlm.nih.gov/public/Visible-Human/Male-Images/PNG_format/head/index.html)
+
+First import the CT data as described in [step by step](step_by_step.md). Then import the anatomical images, but unlike before, this time from the Geometry Nodes menu of the existing container (not the top menu), click **Bioxel Nodes > Import Volumetric Data (Init) > as Color**, locate to the unzipped folder, and select any .png file (do not multi-select, and do not select the folder). This way the imported layer will be in the same container as the previous CT data. You can also import by dragging it into the container geometry node interface instead of the 3D Viewport interface. Also note that **as Color** (not as Scalar) is clicked because the anatomical images are RGB data.
+
+![alt text](assets/advanced_usage/image.png)
+
+Let's take more time in the import options this time 🫡, first let's talk about what the **Original Spacing** is in the options, you can simply think of it as the original "pixel size" of a image, since the volume is 3D, its pixels (i.e., voxels) are cuboids with a length, width, and height rather than 2D rectangles. And their length, width, and height size is the **Spacing**.
+
+Normally, Bioxel Nodes can read the spacing from the data header, and you don't need to fill in the value, but there is no record of that in any PNG image, so you need to input it manually. in the official description of the VHP, it is mentioned that each pixel of the anatomical images corresponds to the size of .33mm, and the thickness of each slice is 1mm, so the Original Spacing of the anatomical images should be set to `(0.33, 0.33, 1)`.
+
+However, the file I provided is scaled by 1/4 for each image, so the X and Y axes need to be multiplied by 4. So the final Original Spacing should be set to `(1.33, 1.33, 1)`, which should be understandable, right? (If you are importing an official file, then it should still be set to `(0.33, 0.33, 1)`)
+Layer Name should be set to "Anatomical Images", other options remain default, click Ok.
+
+![alt text](assets/advanced_usage/image-1.png)
+
+After importing, connect the "Cutout by Hue" node (Add > Bioxel Nodes > Component > Cutout by Hue) after the newly created "Fetch Layer" node, and turn on the Slice Viewer mode preview, as shown below.
+
+![alt text](assets/advanced_usage/image-2.png)
+
+In addition to spacing, the Dicom file also records the subject's position and orientation, but those information is apparently not recorded in PNG format. This results in a mismatch between the CT data and the anatomical images in position. We need to manually align this two layers: First, set the threshold of the "Cutout by Threshold" node to 0.2 so that the full head can be cutouted and displayed. Then add "ReCenter" node before "Cutout by Hue" node and "Cutout by Threshold" node each, then add Locater to the "anatomical images" workflow (see [step by step](step_by_step.md) for details), and finally add "Join Component" node (Add > Bioxel Nodes > Component > Join Component), and connect them as shown below, with the parameters set as shown.
+
+![alt text](assets/advanced_usage/image-3.png)
+
+The "Join Component" node allows you to merge two components together. Move and rotate the Locater object so that the two components are exactly the same in position. If you're having trouble matching them up, here's the exact transform values to fill in the Locater object properties.
+
+![alt text](assets/advanced_usage/image-4.png)
+
+Next let's cutout the muscles individually.
+
+First let's talk about the "Cutout by Hue" node. Literally, it cutout regions by hue of color. If you select this node and press "M" key to temporarily mute it, you'll see that the data becomes a cube with blue parts in Slice Viewer mode. the default value of Hue in the "Cutout by Hue" node is red, meaning that the node retains areas of the body that are close to red, and strip out the blue, which is on the opposite side of the red in the hue ring, leaving the human body parts.
+
+If you turn down the value of Sensitivity, you'll see that the visabile part is decreasing, leaving only the part more closer to red, and the muscle happens to be red, so we can easily cutout the muscle. The color of the specimen tissue is not as vibrant as it is in the live state, and we can fine-tune the color to restore the vibrancy by using the "Set Color by Color" node (Add > Bioxel Nodes > Property > Set Color by Color).
+
+To finally put it all together, connect and set the nodes as shown below, where the two colors in "Set Color by Ramp 2" node are `E7D2C5` and `FFEDEC`. If everything is working correctly, you'll get the rendering below.
+
+![alt text](assets/advanced_usage/image-5.png)
+
+You can also add "Transfrom" and "Cutter" nodes at the end and all components.
+
+![alt text](assets/advanced_usage/image-6.png)
+
+The multimodal data of VHP do not have any deformation or scaling differences, but only positional differences, so all data can be aligned easily. However, in most cases, the differences of different modalities are so great that they need to be registered first, which is not possible with Bioxel Nodes at the moment (but it is in plan). Nevertheless, you can build different components based on the same layer and combine them together. For example, based on the CT data, with the "Cutout by Range" node, you can eliminate the low value regions (fat), eliminate the high value regions (bone), and you can still get the muscle. And then attach it to the skull.
+
+![alt text](assets/advanced_usage/image-7.png)
+
+However, the CT values of brain and muscle are very close to each other, so it is extremely difficult to separate the brain from the muscle by threshold. So how should cutout the brain?
+
+## Cutout the Brain
+
+We can use AI technology to realize the division of brain regions, this process is called Segmentation, and the brain regions are as label. There are many models and methods for medical image segmentation, here we recommend [Total Segmentator](https://github.com/wasserth/TotalSegmentator).
+
+It is an out-of-the-box CT/MRI medical image segmentation Python library. You can deploy Total Segmentator locally or process your data through the official online site [https://totalsegmentator.com](https://totalsegmentator.com).
+
+Let me demonstrate the operation, we are still using the CT data from VHP. Click on "Drop DICOM.zip or ..." and select the VHP_M_CT_Head.zip file. Enter "brain" below "Selected task", press Enter to confirm. Finally click "Process data" button.
+
+![alt text](assets/advanced_usage/image-8.png)
+
+Wait for the uploading and processing, after all, you will be redirected to the following page, click "Download results" button, download and unzip segmentations.zip to any folder directory.
+
+![alt text](assets/advanced_usage/image-9.png)
+
+In case you can't get the brain segment (label), you can download it directly (without unzipping it).
+
+[VHP_M_CT_Head_Brain.nii.gz](https://drive.google.com/file/d/1KGiZ3G11YLXkGszSrvWQ9kTF4TMpxUPd/view?usp=drive_link)
+
+Next we import the brain segment (label) into the container in the same way as we imported the anatomical imagess(under the same container), but this time selecting **as Label**, with the Layer Name set to "Brain", and leaving the other options as default. Once the import is complete, a new "Fetch Layer" node will be added. Create and set the node as shown below, and you should be able to see the surface of brain.
+
+![alt text](assets/advanced_usage/image-10.png)
+
+Do you see the "step" like shape on surface? this is due to the low precision of the AI segmentation results. So How to addressing the issue? Select the Fetch Layer node of the brain label, right-click to pop up menu, click **Bioxel Nodes > Resample Value**, in the dialog box, change the "Smooth Size" to 3 or higher (the higher it is, the slower the calculation will be), click OK and wait for the calculation to finish. When it is done, a new layer will be added, replace the original one, is it smoother? The following figure lists different levels of smoothing.
+
+![alt text](assets/advanced_usage/image-11.png)
+
+The smoother it is, the more comfortable it looks, but it also means that more details are lost and the calculation is slower.
+
+But if you cut the brain, you will find that the cross-section is homogeneous, this is because the label type layer is does not contain any modality data itself. Bioxel Nodes provides a function to fill in any layer values by label, if you set the value below brain tissue in the non-brain region of CT data, then any "Cutout" node will only keep the brain region.
+
+The operation is like this, select the "Fetch Layer" node of the CT data, right-click to pop up the menu, click **Bioxel Nodes > Fill Value by Label**, in the dialog box, Label is set to the newly imported brain label layer, Fill Value is set to -100 (as long as it is less than the Hu value of the brain tissue), click OK. wait for the data processing, a new data layer will be added to the container when it is finished.
+
+As shown in the following figure, connect the nodes and set the node parameters, in which the two colors of "Set Color by Ramp 2" node are `B26267` and `EBC5B7`, and the "Cutout by Range" and "Set Color by Ramp 2" node are changed to "Value" mode (the default is "Factor" mode), because the maximum and minimum values of the brain are too close to each other and difficult to adjust in "Factor" mode. To make the brain tissue look more transparent, I add the "Set Properties" (Add > Bioxel Nodes > Property > Set Properties) node at the end and changed the "Density" to 0.5.
+
+![alt text](assets/advanced_usage/image-12.png)
+
+(Still feel not smooth enough? It's really hard to get rid of "step" surface completely at the moment)
+
+Now the brain is done. Finally we combine all together and you get something like the following.
+
+![alt text](assets/advanced_usage/image-13.png)
+
+🤗 If you've followed the docs up to this point, give yourself a round of applause, you've mastered this addon! If you have trouble following the docs instruction, you can download the project files to understand how the nodes work.
+
+[VHP.zip](https://drive.google.com/file/d/1EHB7sxNSvJNwmoTfFnpyOSsm2M_2Y0hO/view?usp=sharing)
+
+AI segmentation is an essential part of volumetric data visualization. Therefore, the future Bioxel Nodes will integrate some commonly used AI segmentation models, so that users can complete the volumetric data visualization in place!