feat: improving the user experience

bioxelnodes/bioxel/layer.py

@@ -2,7 +2,6 @@ import copy
 import numpy as np
 
 from . import scipy
-from . import skimage as ski
 from . import scipy as ndi
 
 # 3rd-party
@@ -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.minimum_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.minimum_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,)
@@ -97,12 +100,11 @@ 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
-        order = 0 if self.dtype == bool else 1
 
         # # TXYZC > TXYZ
         # if self.kind in ['label', 'scalar']:
@@ -121,15 +123,22 @@ class Layer():
             #                    shape,
             #                    preserve_range=True,
             #                    anti_aliasing=data.dtype.kind != "b")
+            frame = data[f, :, :, :, :]
+            if smooth > 0:
+                frame = scipy.median_filter(frame.astype(np.float32),
+                                            mode="nearest",
+                                            size=smooth)
 
             factors = np.divide(self.shape, shape)
             zoom_factors = [1 / f for f in factors]
-            frame = ndi.zoom(data[f, :, :, :, :],
+            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)

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
@@ -166,7 +165,7 @@ def remove_end_str(string: str, end: str):
     return string
 
 
-def parse_volumetric_data(data_file: str, series_id="", progress_callback=None) -> Layer:
+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:

bioxelnodes/bioxelutils/common.py

@@ -1,5 +1,10 @@
+from ast import literal_eval
+from pathlib import Path
 import bpy
 
+from ..constants import NODE_LIB_FILEPATH, VERSION
+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]
@@ -48,20 +53,65 @@ def get_container_obj(current_obj):
     return None
 
 
-def get_layer_prop_value(layer_obj: bpy.types.Object, prop: str):
+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]
-    value = layer_node.inputs[prop].default_value
+    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)
-    if type(value).__name__ == "float":
+    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):
@@ -95,6 +145,7 @@ def get_all_layer_objs():
 
     return layer_objs
 
+
 def add_driver(target, target_prop, var_sources, expression):
     driver = target.driver_add(target_prop)
     is_vector = isinstance(driver, list)
@@ -126,3 +177,69 @@ def add_direct_driver(target, target_prop, source, 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 is_incompatible():
+    if get_file_prop("addon_version") is None:
+        for node_group in bpy.data.node_groups:
+            if node_group.name.startswith("BioxelNodes"):
+                return True
+    else:
+        addon_version = literal_eval(get_file_prop("addon_version"))
+        if addon_version[0] != VERSION[0]\
+                or addon_version[1] != VERSION[1]:
+            return True
+
+    return False
+
+def local_lib_not_updated():
+    use_local = False
+    for node_group in bpy.data.node_groups:
+        if node_group.name.startswith("BioxelNodes"):
+            node_group_lib = node_group.library
+            if node_group_lib:
+                abs_filepath = bpy.path.abspath(node_group_lib.filepath)
+                _local_lib_file = Path(abs_filepath).resolve().as_posix()
+                if _local_lib_file != NODE_LIB_FILEPATH.as_posix():
+                    use_local = True
+                    break
+    
+    addon_version = literal_eval(get_file_prop("addon_version"))
+    not_update = addon_version != VERSION
+    return use_local and not_update

bioxelnodes/bioxelutils/container.py

@@ -6,12 +6,12 @@ from mathutils import Matrix, Vector
 
 
 from .layer import Layer, layer_to_obj, obj_to_layer
-from ..nodes import custom_nodes
+from .common import (get_container_layer_objs,
-from .utils import (get_container_layer_objs,
                      get_layer_prop_value,
                      get_nodes_by_type,
                      move_node_to_node)
-
+from .node import add_node_to_graph
+from ..utils import get_use_link
 
 NODE_TYPE = {
     "label": "BioxelNodes_MaskByLabel",
@@ -82,13 +82,17 @@ def add_layers(layers: list[Layer],
                cache_dir: str):
 
     node_group = container_obj.modifiers[0].node_group
+    try:
         output_node = get_nodes_by_type(node_group,
                                         'NodeGroupOutput')[0]
+    except:
+        output_node = node_group.nodes.new("NodeGroupOutput")
 
     for i, layer in enumerate(layers):
         layer_obj = layer_to_obj(layer, container_obj, cache_dir)
-        fetch_node = custom_nodes.add_node(node_group,
+        fetch_node = add_node_to_graph("FetchLayer",
-                                           "BioxelNodes_FetchLayer")
+                                       node_group,
+                                       get_use_link())
         fetch_node.label = get_layer_prop_value(layer_obj, "name")
         fetch_node.inputs[0].default_value = layer_obj
 
@@ -104,6 +108,7 @@ def add_layers(layers: list[Layer],
 
 def container_to_obj(container: Container,
                      scene_scale: float,
+                     step_size: float,
                      cache_dir: str):
     # Wrapper a Container
 
@@ -134,11 +139,26 @@ 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
 
     modifier = container_obj.modifiers.new("GeometryNodes", 'NODES')
     node_group = bpy.data.node_groups.new('GeometryNodes', 'GeometryNodeTree')
-    node_group.interface.new_socket(name="Component",
+    node_group.interface.new_socket(name="Output",
                                     in_out="OUTPUT",
                                     socket_type="NodeSocketGeometry")
     modifier.node_group = node_group

bioxelnodes/bioxelutils/layer.py

@@ -7,10 +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 .utils import (get_layer_prop_value,
+from ..utils import get_use_link
-                    move_node_between_nodes, add_direct_driver)
+from .node import add_node_to_graph
+from .common import (get_layer_prop_value,
+                     move_node_between_nodes)
 
 
 def obj_to_layer(layer_obj: bpy.types.Object):
@@ -26,7 +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)
@@ -34,7 +39,11 @@ 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
 
@@ -137,13 +146,12 @@ def layer_to_obj(layer: Layer,
 
     layer_data = bpy.data.volumes.new(layer_display_name)
     layer_data.render.space = 'WORLD'
-    layer_data.render.step_size = container_obj.scale[0] * layer.bioxel_size[0]
+    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])
 
-    # add_direct_driver(layer_data, "render.step_size",
-    #                   container_obj, "scale[0]")
-
     if layer.frame_count > 1:
         layer_data.is_sequence = True
         layer_data.frame_duration = layer.frame_count
@@ -164,8 +172,7 @@ def layer_to_obj(layer: Layer,
                                     socket_type="NodeSocketGeometry")
     modifier.node_group = node_group
 
-    layer_node = custom_nodes.add_node(node_group,
+    layer_node = add_node_to_graph("_Layer", node_group, get_use_link())
-                                       "BioxelNodes__Layer")
 
     layer_node.inputs['name'].default_value = layer.name
     layer_node.inputs['shape'].default_value = layer.shape
@@ -176,11 +183,12 @@ 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

bioxelnodes/bioxelutils/node.py

@@ -0,0 +1,68 @@
+from pathlib import Path
+import shutil
+import bpy
+
+from .common import get_file_prop, set_file_prop
+from ..exceptions import Incompatible, NoFound
+
+from ..constants import NODE_LIB_FILEPATH, VERSION
+
+
+def get_node_group(node_type: str, use_link=True):
+    # unannotate below for local debug in node lib file.
+    # node_group = bpy.data.node_groups[node_type]
+    # return node_group
+
+    if get_file_prop("addon_version") is None:
+        set_file_prop("addon_version", VERSION)
+
+    local_lib_file = None
+    addon_lib_file = NODE_LIB_FILEPATH.as_posix()
+
+    for node_group in bpy.data.node_groups:
+        if node_group.name.startswith("BioxelNodes"):
+            node_group_lib = node_group.library
+            if node_group_lib:
+                abs_filepath = bpy.path.abspath(node_group_lib.filepath)
+                _local_lib_file = Path(abs_filepath).resolve().as_posix()
+                if _local_lib_file != addon_lib_file:
+                    local_lib_file = _local_lib_file
+                    break
+
+    # local lib first
+    lib_file = local_lib_file or addon_lib_file
+    bpy.ops.wm.append('EXEC_DEFAULT',
+                      directory=f"{lib_file}/NodeTree",
+                      filename=node_type,
+                      link=use_link,
+                      use_recursive=True,
+                      do_reuse_local_id=True)
+    node_group = bpy.data.node_groups.get(node_type)
+
+    if node_group is None:
+        raise NoFound('No custom node found')
+
+    return node_group
+
+
+def assign_node_group(node, node_type: str):
+    node.node_tree = bpy.data.node_groups[node_type]
+    node.width = 200.0
+    node.name = node_type
+    return node
+
+
+def add_node_to_graph(node_name: str, node_group, use_link=True):
+    node_type = f"BioxelNodes_{node_name}"
+
+    # Deselect all nodes first
+    for node in node_group.nodes:
+        if node.select:
+            node.select = False
+
+    get_node_group(node_type, use_link)
+    node = node_group.nodes.new("GeometryNodeGroup")
+    assign_node_group(node, node_type)
+
+    node.show_options = False
+    return node

bioxelnodes/blender_manifest.toml

@@ -1,7 +1,7 @@
 schema_version = "1.0.0"
 
 id = "bioxelnodes"
-version = "0.4.0"
+version = "1.0.0"
 name = "Bioxel Nodes"
 tagline = "For scientific volumetric data visualization in Blender"
 maintainer = "Ma Nan <icrdr2010@outlook.com>"

bioxelnodes/constants.py

@@ -1,8 +1,9 @@
-
 from pathlib import Path
-from .customnodes import CustomNodes
 
-NODE_FILE = "BioxelNodes_4.2"
+VERSION = (1, 0, 0)
+NODE_LIB_FILENAME = "BioxelNodes_v1.0.x"
+NODE_LIB_FILEPATH = Path(Path(__file__).parent,
+                         f"assets/Nodes/{NODE_LIB_FILENAME}.blend").resolve()
 
 MENU_ITEMS = [
     {
@@ -12,34 +13,40 @@ MENU_ITEMS = [
             {
                 'label': 'Cutout by Threshold',
                 'icon': 'EMPTY_SINGLE_ARROW',
-                'node_type': 'BioxelNodes_CutoutByThreshold',
+                'name': 'CutoutByThreshold',
-                'node_description': ''
+                'description': ''
             },
             {
                 'label': 'Cutout by Range',
                 'icon': 'IPO_CONSTANT',
-                'node_type': 'BioxelNodes_CutoutByRange',
+                'name': 'CutoutByRange',
-                'node_description': ''
+                'description': ''
             },
             {
                 'label': 'Cutout by Color',
                 'icon': 'COLOR',
-                'node_type': 'BioxelNodes_CutoutByColor',
+                'name': 'CutoutByColor',
-                'node_description': ''
+                'description': ''
             },
             "separator",
             {
                 'label': 'To Surface',
                 'icon': 'MESH_DATA',
-                'node_type': 'BioxelNodes_ToSurface',
+                'name': 'ToSurface',
-                'node_description': ''
+                'description': ''
             },
             {
                 'label': 'Join Component',
                 'icon': 'CONSTRAINT_BONE',
-                'node_type': 'BioxelNodes_JoinComponent',
+                'name': 'JoinComponent',
-                'node_description': ''
+                'description': ''
             },
+            {
+                'label': 'Slice',
+                'icon': 'TEXTURE',
+                'name': 'Slice',
+                'description': ''
+            }
         ]
     },
     {
@@ -49,59 +56,46 @@ MENU_ITEMS = [
             {
                 'label': 'Set Properties',
                 'icon': 'PROPERTIES',
-                'node_type': 'BioxelNodes_SetProperties',
+                'name': 'SetProperties',
-                'node_description': ''
+                'description': ''
             },
             "separator",
             {
                 'label': 'Set Color',
                 'icon': 'IPO_SINE',
-                'node_type': 'BioxelNodes_SetColor',
+                'name': 'SetColor',
-                'node_description': ''
+                'description': ''
             },
             {
                 'label': 'Set Color by Color',
                 'icon': 'IPO_QUINT',
-                'node_type': 'BioxelNodes_SetColorByColor',
+                'name': 'SetColorByColor',
-                'node_description': ''
+                'description': ''
             },
             {
                 'label': 'Set Color by Ramp 2',
                 'icon': 'IPO_QUAD',
-                'node_type': 'BioxelNodes_SetColorByRamp2',
+                'name': 'SetColorByRamp2',
-                'node_description': ''
+                'description': ''
             },
             {
                 'label': 'Set Color by Ramp 3',
                 'icon': 'IPO_CUBIC',
-                'node_type': 'BioxelNodes_SetColorByRamp3',
+                'name': 'SetColorByRamp3',
-                'node_description': ''
+                'description': ''
             },
             {
                 'label': 'Set Color by Ramp 4',
                 'icon': 'IPO_QUART',
-                'node_type': 'BioxelNodes_SetColorByRamp4',
+                'name': 'SetColorByRamp4',
-                'node_description': ''
+                'description': ''
             },
             {
                 'label': 'Set Color by Ramp 5',
                 'icon': 'IPO_QUINT',
-                'node_type': 'BioxelNodes_SetColorByRamp5',
+                'name': 'SetColorByRamp5',
-                'node_description': ''
+                'description': ''
-            },
+            }
-            # "separator",
-            # {
-            #     'label': 'Color Presets',
-            #     'icon': 'COLOR',
-            #     'node_type': 'BioxelNodes_ColorPresets',
-            #     'node_description': ''
-            # }
-            # {
-            #     'label': 'Color Presets MRI',
-            #     'icon': 'COLOR',
-            #     'node_type': 'BioxelNodes_ColorPresets_MRI',
-            #     'node_description': ''
-            # },
         ]
     },
     {
@@ -111,39 +105,45 @@ MENU_ITEMS = [
             {
                 'label': 'Membrane Shader',
                 'icon': 'NODE_MATERIAL',
-                'node_type': 'BioxelNodes_AssignMembraneShader',
+                'name': 'AssignMembraneShader',
-                'node_description': ''
+                'description': ''
             },
             {
                 'label': 'Solid Shader',
                 'icon': 'SHADING_SOLID',
-                'node_type': 'BioxelNodes_AssignSolidShader',
+                'name': 'AssignSolidShader',
-                'node_description': ''
+                'description': ''
             },
             {
                 'label': 'Slime Shader',
                 'icon': 'OUTLINER_DATA_META',
-                'node_type': 'BioxelNodes_AssignSlimeShader',
+                'name': 'AssignSlimeShader',
-                'node_description': ''
+                'description': ''
             },
-            "separator",
+
-            {
+        ]
-                'label': 'Inflate',
-                'icon': 'OUTLINER_OB_META',
-                'node_type': 'BioxelNodes_M_Inflate',
-                'node_description': ''
     },
     {
-                'label': 'Smooth',
+        'label': 'Transform',
-                'icon': 'MOD_SMOOTH',
+        'icon': 'EMPTY_AXIS',
-                'node_type': 'BioxelNodes_M_Smooth',
+        'items': [
-                'node_description': ''
+            {
+                'label': 'Transform',
+                'icon': 'EMPTY_AXIS',
+                'name': 'Transform',
+                'description': ''
             },
             {
-                'label': 'Remove Small Island',
+                'label': 'Transform Parent',
-                'icon': 'FORCE_LENNARDJONES',
+                'icon': 'ORIENTATION_PARENT',
-                'node_type': 'BioxelNodes_M_RemoveSmallIsland',
+                'name': 'TransformParent',
-                'node_description': ''
+                'description': ''
+            },
+            {
+                'label': 'ReCenter',
+                'icon': 'PROP_CON',
+                'name': 'ReCenter',
+                'description': ''
             }
         ]
     },
@@ -154,21 +154,21 @@ MENU_ITEMS = [
             {
                 'label': 'Cut',
                 'icon': 'MOD_BEVEL',
-                'node_type': 'BioxelNodes_Cut',
+                'name': 'Cut',
-                'node_description': ''
+                'description': ''
             },
             "separator",
             {
                 'label': 'Primitive Cutter',
                 'icon': 'MOD_LINEART',
-                'node_type': 'BioxelNodes_PrimitiveCutter',
+                'name': 'PrimitiveCutter',
-                'node_description': ''
+                'description': ''
             },
             {
                 'label': 'Object Cutter',
                 'icon': 'MESH_PLANE',
-                'node_type': 'BioxelNodes_ObjectCutter',
+                'name': 'ObjectCutter',
-                'node_description': ''
+                'description': ''
             }
         ]
     },
@@ -177,41 +177,48 @@ MENU_ITEMS = [
         'icon': 'MODIFIER',
         'items': [
             {
-                'label': 'Pick Mesh',
+                'label': 'Pick Surface',
                 'icon': 'OUTLINER_OB_MESH',
-                'node_type': 'BioxelNodes_PickMesh',
+                'name': 'PickSurface',
-                'node_description': ''
+                'description': ''
             },
             {
                 'label': 'Pick Volume',
                 'icon': 'OUTLINER_OB_VOLUME',
-                'node_type': 'BioxelNodes_PickVolume',
+                'name': 'PickVolume',
-                'node_description': ''
+                'description': ''
+            },
+            {
+                'label': 'Pick Shape Wire',
+                'icon': 'FILE_VOLUME',
+                'name': 'PickShapeWire',
+                'description': ''
             },
             {
                 'label': 'Pick Bbox Wire',
                 'icon': 'MESH_CUBE',
-                'node_type': 'BioxelNodes_PickBboxWire',
+                'name': 'PickBboxWire',
-                'node_description': ''
+                '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': ''
             }
-            
         ]
     }
 ]
-
-
-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/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

@@ -1,117 +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="",
-        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:
-            return node_tree
-        else:
-            raise RuntimeError('No custom node found')
-
-
-    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

@@ -1,46 +1,70 @@
-from pathlib import Path
 import bpy
 
-from .operators.utils import get_layer_item_label
+from .constants import MENU_ITEMS, NODE_LIB_FILENAME
-from .bioxelutils.utils import (get_container_obj,
+from .node_menu import NodeMenu
-                                get_container_objs_from_selection,
+
-                                get_container_layer_objs,
+from .bioxelutils.common import (get_container_obj,
+                                 get_container_layer_objs, get_layer_label,
                                  get_layer_prop_value)
-from .operators.layer import (FetchLayerMenu, FetchLayer,
+from .operators.layer import (FetchLayer, RelocateLayer, RetimeLayer, RenameLayer,
-                              RemoveLayer, RemoveMissingLayers, RenameLayer, ResampleScalar, SaveLayerCache,
+                              RemoveSelectedLayers, SaveSelectedLayersCache,
-                              SignScalar, CombineLabels,
+                              ResampleLayer, SignScalar, CombineLabels,
-                              FillByLabel, FillByThreshold, FillByRange, get_selected_objs_in_node_tree)
+                              FillByLabel, FillByThreshold, FillByRange)
-from .operators.container import (SaveAllLayerCaches, SaveContainer, LoadContainer,
+from .operators.container import (AddLocator, AddSlicer, ExtractShapeWire,
+                                  SaveContainerLayersCache, RemoveContainerMissingLayers,
+                                  SaveContainer, LoadContainer,
                                   AddPieCutter, AddPlaneCutter,
                                   AddCylinderCutter, AddCubeCutter, AddSphereCutter,
-                                  PickBboxWire, PickMesh, PickVolume, ScaleContainer)
+                                  ExtractBboxWire, ExtractSurface, ExtractVolume, ContainerProps)
+
 from .operators.io import (ImportAsLabel, ImportAsScalar, ImportAsColor)
-from .operators.misc import (CleanAllCaches,
+from .operators.misc import (CleanTemp,
-                             ReLinkNodes, RenderSettingPreset, SaveStagedData, SliceViewer)
+                             ReLinkNodeLib, RemoveAllMissingLayers, RenderSettingPreset, SaveAllLayersCache, SaveNodeLib, SliceViewer)
 
 
-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(ExtractSurface.bl_idname)
-        layout.operator(PickVolume.bl_idname)
+        layout.operator(ExtractVolume.bl_idname)
-        layout.operator(PickBboxWire.bl_idname)
+        layout.operator(ExtractShapeWire.bl_idname)
+        layout.operator(ExtractBboxWire.bl_idname)
 
 
 class AddCutterMenu(bpy.types.Menu):
     bl_idname = "BIOXELNODES_MT_CUTTERS"
-    bl_label = "Add a Object Cutter"
+    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):
@@ -60,7 +84,7 @@ class ImportLayerMenu(bpy.types.Menu):
 
 class AddLayerMenu(bpy.types.Menu):
     bl_idname = "BIOXELNODES_MT_ADDLAYER"
-    bl_label = "Import Volumetric Data (Add to)"
+    bl_label = "Import Volumetric Data (Add)"
     bl_icon = "FILE_NEW"
 
     def draw(self, context):
@@ -79,31 +103,37 @@ class ModifyLayerMenu(bpy.types.Menu):
     bl_icon = "FILE_NEW"
 
     def draw(self, context):
-        layer_objs = get_selected_objs_in_node_tree(context)
-        if len(layer_objs) > 0:
-            active_obj_name = layer_objs[0].name
-        else:
-            active_obj_name = ""
-
         layout = self.layout
-        op = layout.operator(ResampleScalar.bl_idname,
+        layout.operator(SignScalar.bl_idname,
-                             icon=ResampleScalar.bl_icon)
-        op.layer_obj_name = active_obj_name
-        op = layout.operator(SignScalar.bl_idname,
                         icon=SignScalar.bl_icon)
-        op.layer_obj_name = active_obj_name
+        layout.operator(FillByThreshold.bl_idname,
-        op = layout.operator(FillByThreshold.bl_idname,
                         icon=FillByThreshold.bl_icon)
-        op.layer_obj_name = active_obj_name
+        layout.operator(FillByRange.bl_idname,
-        op = layout.operator(FillByRange.bl_idname,
                         icon=FillByRange.bl_icon)
-        op.layer_obj_name = active_obj_name
+        layout.operator(FillByLabel.bl_idname,
-        op = layout.operator(FillByLabel.bl_idname,
                         icon=FillByLabel.bl_icon)
-        op.layer_obj_name = active_obj_name
+        layout.operator(CombineLabels.bl_idname,
-        op = layout.operator(CombineLabels.bl_idname,
                         icon=CombineLabels.bl_icon)
-        op.layer_obj_name = active_obj_name
+
+
+class ReLinkNodeLibMenu(bpy.types.Menu):
+    bl_idname = "BIOXELNODES_MT_RELINK"
+    bl_label = "Relink Node Library"
+
+    def draw(self, context):
+        layout = self.layout
+        versions = [{"label": "v0.3.x", "filename": "BioxelNodes_v0.3.x"},
+                    {"label": "v0.2.x", "filename": "BioxelNodes_v0.2.x"},
+                    {"label": "v0.1.x", "filename": "BioxelNodes_v0.1.x"}]
+
+        op = layout.operator(ReLinkNodeLib.bl_idname,
+                             text="Current Version")
+        op.node_lib_filename = NODE_LIB_FILENAME
+        layout.separator()
+        for version in versions:
+            op = layout.operator(ReLinkNodeLib.bl_idname,
+                                 text=version["label"])
+            op.node_lib_filename = version["filename"]
 
 
 class RenderSettingMenu(bpy.types.Menu):
@@ -118,6 +148,15 @@ class RenderSettingMenu(bpy.types.Menu):
             op.preset = k
 
 
+class DangerZoneMenu(bpy.types.Menu):
+    bl_idname = "BIOXELNODES_MT_DANGER"
+    bl_label = "Danger Zone"
+
+    def draw(self, context):
+        layout = self.layout
+        layout.operator(CleanTemp.bl_idname)
+
+
 class BioxelNodesTopbarMenu(bpy.types.Menu):
     bl_idname = "BIOXELNODES_MT_TOPBAR"
     bl_label = "Bioxel Nodes"
@@ -130,9 +169,15 @@ class BioxelNodesTopbarMenu(bpy.types.Menu):
         layout.operator(LoadContainer.bl_idname)
 
         layout.separator()
-        layout.operator(SaveStagedData.bl_idname)
+        layout.operator(SaveAllLayersCache.bl_idname)
-        layout.operator(ReLinkNodes.bl_idname)
+        layout.operator(RemoveAllMissingLayers.bl_idname)
-        layout.operator(CleanAllCaches.bl_idname)
+
+        layout.separator()
+        layout.operator(SaveNodeLib.bl_idname)
+        layout.menu(ReLinkNodeLibMenu.bl_idname)
+
+        layout.separator()
+        layout.menu(DangerZoneMenu.bl_idname)
 
         layout.separator()
         layout.menu(RenderSettingMenu.bl_idname)
@@ -143,51 +188,66 @@ def TOPBAR(self, context):
     layout.menu(BioxelNodesTopbarMenu.bl_idname)
 
 
-class BioxelNodesNodeMenu(bpy.types.Menu):
+class NodeHeadMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_NODE"
+    bl_idname = "BIOXELNODES_MT_NODE_HEAD"
     bl_label = "Bioxel Nodes"
     bl_icon = "FILE_VOLUME"
 
     def draw(self, context):
-        layer_objs = get_selected_objs_in_node_tree(context)
-        if len(layer_objs) > 0:
-            active_obj_name = layer_objs[0].name
-        else:
-            active_obj_name = ""
 
         layout = self.layout
-        layout.separator()
         layout.menu(AddLayerMenu.bl_idname,
                     icon=AddLayerMenu.bl_icon)
-        layout.separator()
         layout.operator(SaveContainer.bl_idname)
+
         layout.separator()
-        layout.operator(ScaleContainer.bl_idname)
+        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.menu(PickFromContainerMenu.bl_idname)
-        layout.operator(SaveAllLayerCaches.bl_idname,
-                        icon=SaveAllLayerCaches.bl_icon)
-        layout.operator(RemoveMissingLayers.bl_idname,
-                        icon=RemoveMissingLayers.bl_icon)
 
         layout.separator()
         layout.menu(FetchLayerMenu.bl_idname)
-        op = layout.operator(SaveLayerCache.bl_idname,
-                             icon=SaveLayerCache.bl_icon)
-        op.layer_obj_name = active_obj_name
-        op = layout.operator(RenameLayer.bl_idname,
-                             icon=RenameLayer.bl_icon)
-        op.layer_obj_name = active_obj_name
 
-        op = layout.operator(RemoveLayer.bl_idname,
+
-                             icon=RemoveLayer.bl_icon)
+class NodeContextMenu(bpy.types.Menu):
-        op.layer_obj_name = active_obj_name
+    bl_idname = "BIOXELNODES_MT_NODE_CONTEXT"
+    bl_label = "Bioxel Nodes"
+    bl_icon = "FILE_VOLUME"
+
+    def draw(self, context):
+        layout = self.layout
+        layout.operator(SaveSelectedLayersCache.bl_idname,
+                        icon=SaveSelectedLayersCache.bl_icon)
+        layout.operator(RemoveSelectedLayers.bl_idname)
 
         layout.separator()
-        layout.menu(ModifyLayerMenu.bl_idname)
+        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(self, context):
+def NODE_CONTEXT(self, context):
     container_obj = context.object
     is_geo_nodes = context.area.ui_type == "GeometryNodeTree"
     is_container = get_container_obj(container_obj)
@@ -197,10 +257,23 @@ def NODE(self, context):
 
     layout = self.layout
     layout.separator()
-    layout.menu(BioxelNodesNodeMenu.bl_idname)
+    layout.menu(NodeContextMenu.bl_idname)
 
 
-def NODE_PT(self, context):
+def NODE_HEAD(self, context):
+    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):
     container_obj = context.object
     is_geo_nodes = context.area.ui_type == "GeometryNodeTree"
     is_container = get_container_obj(container_obj)
@@ -216,20 +289,19 @@ def NODE_PT(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
     layer_list.clear()
 
     for layer_obj in get_container_layer_objs(container_obj):
         layer_item = layer_list.add()
-        layer_item.label = get_layer_item_label(context, layer_obj)
+        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", "min", "max", ]])
+                                          for prop in ["kind",
-
+                                                       "bioxel_size",
-    if len(layer_list) > 0 and layer_list_active != -1 and layer_list_active < len(layer_list):
+                                                       "shape",
-        active_obj_name = layer_list[layer_list_active].obj_name
+                                                       "frame_count",
-    else:
+                                                       "channel_count",
-        active_obj_name = ""
+                                                       "min", "max"]])
 
     layout = self.layout
     layout.label(text="Layer List")
@@ -243,48 +315,41 @@ def NODE_PT(self, context):
                         item_dyntip_propname="info_text",
                         rows=20)
 
-    sidebar = split.column(align=True)
+    # sidebar = split.column(align=True)
-    sidebar.menu(AddLayerMenu.bl_idname,
+    # sidebar.menu(AddLayerMenu.bl_idname,
-                 icon=AddLayerMenu.bl_icon, text="")
+    #              icon=AddLayerMenu.bl_icon, text="")
 
-    sidebar.operator(SaveAllLayerCaches.bl_idname,
+    # sidebar.operator(SaveContainerLayersCache.bl_idname,
-                    icon=SaveAllLayerCaches.bl_icon, text="")
+    #                  icon=SaveContainerLayersCache.bl_icon, text="")
-    sidebar.operator(RemoveMissingLayers.bl_idname,
+    # sidebar.operator(RemoveContainerMissingLayers.bl_idname,
-                     icon=RemoveMissingLayers.bl_icon, text="")
+    #                  icon=RemoveContainerMissingLayers.bl_icon, text="")
 
-    sidebar.separator()
+    # sidebar.separator()
-    op = sidebar.operator(FetchLayer.bl_idname,
+    # sidebar.operator(SaveSelectedLayersCache.bl_idname,
-                          icon=FetchLayer.bl_icon, text="")
+    #                  icon=SaveSelectedLayersCache.bl_icon, text="")
-    op.layer_obj_name = active_obj_name
+    # sidebar.operator(RemoveSelectedLayers.bl_idname,
-    op = sidebar.operator(SaveLayerCache.bl_idname,
+    #                  icon=RemoveSelectedLayers.bl_icon, text="")
-                          icon=SaveLayerCache.bl_icon, text="")
-    op.layer_obj_name = active_obj_name
-    op = sidebar.operator(RenameLayer.bl_idname,
-                          icon=RenameLayer.bl_icon, text="")
-    op.layer_obj_name = active_obj_name
-    op = sidebar.operator(RemoveLayer.bl_idname,
-                          icon=RemoveLayer.bl_icon, text="")
-    op.layer_obj_name = active_obj_name
 
-    sidebar.separator()
+    # sidebar.separator()
-    op = sidebar.operator(ResampleScalar.bl_idname,
+    # sidebar.operator(RenameLayer.bl_idname,
-                          icon=ResampleScalar.bl_icon, text="")
+    #                  icon=RenameLayer.bl_icon, text="")
-    op.layer_obj_name = active_obj_name
+    # sidebar.operator(ResampleLayer.bl_idname,
-    op = sidebar.operator(SignScalar.bl_idname,
+    #                  icon=ResampleLayer.bl_icon, text="")
-                          icon=SignScalar.bl_icon, text="")
+    # sidebar.operator(RetimeLayer.bl_idname,
-    op.layer_obj_name = active_obj_name
+    #                  icon=RetimeLayer.bl_icon, text="")
-    op = sidebar.operator(FillByThreshold.bl_idname,
-                          icon=FillByThreshold.bl_icon, text="")
-    op.layer_obj_name = active_obj_name
-    op = sidebar.operator(FillByRange.bl_idname,
-                          icon=FillByRange.bl_icon, text="")
-    op.layer_obj_name = active_obj_name
-    op = sidebar.operator(FillByLabel.bl_idname,
-                          icon=FillByLabel.bl_icon, text="")
-    op.layer_obj_name = active_obj_name
 
-    sidebar.separator()
+    # sidebar.separator()
-    layout.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):
@@ -293,15 +358,24 @@ def VIEW3D_TOPBAR(self, context):
                     icon=SliceViewer.bl_icon, text="")
 
 
+node_menu = NodeMenu(
+    menu_items=MENU_ITEMS
+)
+
+
 def add():
+    node_menu.register()
     bpy.types.VIEW3D_HT_header.append(VIEW3D_TOPBAR)
-    bpy.types.NODE_PT_node_tree_properties.prepend(NODE_PT)
     bpy.types.TOPBAR_MT_editor_menus.append(TOPBAR)
-    bpy.types.NODE_MT_editor_menus.append(NODE)
+    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.VIEW3D_HT_header.remove(VIEW3D_TOPBAR)
-    bpy.types.NODE_PT_node_tree_properties.remove(NODE_PT)
     bpy.types.TOPBAR_MT_editor_menus.remove(TOPBAR)
-    bpy.types.NODE_MT_editor_menus.remove(NODE)
+    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/operators/container.py

@@ -2,17 +2,16 @@ import bpy
 
 import bmesh
 
-from ..nodes import custom_nodes
+from ..utils import get_cache_dir, get_use_link, select_object
-from ..customnodes.nodes import AddCustomNode
 from ..bioxel.io import load_container, save_container
 from ..bioxelutils.container import container_to_obj, obj_to_container
-from ..bioxelutils.utils import (get_container_layer_objs, get_container_obj, 
+from ..bioxelutils.node import add_node_to_graph
-                                 get_layer_prop_value, get_nodes_by_type,
+from ..bioxelutils.common import (get_container_layer_objs, get_container_obj,
+                                  get_nodes_by_type, is_missing_layer,
                                   move_node_between_nodes,
                                   move_node_to_node,
                                   get_all_layer_objs)
-
+from .layer import RemoveLayers, SaveLayersCache
-from .utils import get_cache_dir, select_object
 
 
 class SaveContainer(bpy.types.Operator):
@@ -63,7 +62,7 @@ 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:
@@ -78,7 +77,7 @@ class LoadContainer(bpy.types.Operator):
         return {'RUNNING_MODAL'}
 
 
-class PickObject():
+class ExtractObject():
     bl_options = {'UNDO'}
 
     def execute(self, context):
@@ -92,18 +91,19 @@ class PickObject():
             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,
+                                            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])
 
         select_object(obj)
 
@@ -112,26 +112,34 @@ class PickObject():
         return {'FINISHED'}
 
 
-class PickMesh(bpy.types.Operator, PickObject):
+class ExtractSurface(bpy.types.Operator, ExtractObject):
-    bl_idname = "bioxelnodes.pick_mesh"
+    bl_idname = "bioxelnodes.fetch_mesh"
-    bl_label = "Pick Mesh"
+    bl_label = "Extract Surface"
-    bl_description = "Pick Container Mesh"
+    bl_description = "Extract Surface"
     bl_icon = "OUTLINER_OB_MESH"
-    object_type = "Mesh"
+    object_type = "Surface"
 
 
-class PickVolume(bpy.types.Operator, PickObject):
+class ExtractVolume(bpy.types.Operator, ExtractObject):
     bl_idname = "bioxelnodes.pick_volume"
-    bl_label = "Pick Volume"
+    bl_label = "Extract Volume"
-    bl_description = "Pick Container Volume"
+    bl_description = "Extract Volume"
     bl_icon = "OUTLINER_OB_VOLUME"
     object_type = "Volume"
 
 
-class PickBboxWire(bpy.types.Operator, PickObject):
+class ExtractShapeWire(bpy.types.Operator, ExtractObject):
+    bl_idname = "bioxelnodes.pick_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.pick_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"
 
@@ -162,14 +170,12 @@ class AddCutter():
         elif self.cutter_type == "pie":
             bpy.ops.mesh.primitive_plane_add(
                 size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-            pie = bpy.context.active_object
+            pie_obj = bpy.context.active_object
-            pie.name = "Pie"
+            orig_data = pie_obj.data
-            orig_data = pie.data
 
             # Create mesh
             pie_mesh = bpy.data.meshes.new('Pie')
-
+            pie_obj.data = pie_mesh
-            pie.data = pie_mesh
             bpy.data.meshes.remove(orig_data)
 
             # # Create object
@@ -204,7 +210,19 @@ class AddCutter():
             # bpy.context.view_layer.objects.active = pie
 
         cutter_obj = bpy.context.active_object
-        cutter_obj.location = container_obj.location
+
+        # 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 = self.cutter_type.capitalize()
+        cutter_obj.name = name
+        cutter_obj.data.name = name
         cutter_obj.visible_camera = False
         cutter_obj.visible_diffuse = False
         cutter_obj.visible_glossy = False
@@ -213,6 +231,7 @@ 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)
 
@@ -222,13 +241,16 @@ class AddCutter():
         cut_nodes = get_nodes_by_type(node_group,
                                       'BioxelNodes_Cut')
         if len(cut_nodes) == 0:
-            cutter_node = custom_nodes.add_node(node_group,
+            cutter_node = add_node_to_graph("ObjectCutter",
-                                                "BioxelNodes_ObjectCutter")
+                                            node_group,
+                                            get_use_link())
             cutter_node.inputs[0].default_value = self.cutter_type.capitalize()
             cutter_node.inputs[1].default_value = cutter_obj
 
-            cut_node = custom_nodes.add_node(node_group,
+            cut_node = add_node_to_graph("Cut",
-                                             'BioxelNodes_Cut')
+                                         node_group,
+                                         get_use_link())
+
             output_node = get_nodes_by_type(node_group,
                                             'NodeGroupOutput')[0]
             if len(output_node.inputs[0].links) == 0:
@@ -249,58 +271,20 @@ class AddCutter():
 
             move_node_to_node(cutter_node, cut_node, (-300, -300))
         else:
-            bpy.ops.bioxelnodes.object_cutter('INVOKE_DEFAULT',
+            bpy.ops.bioxelnodes.add_node('EXEC_DEFAULT',
-                                              cutter_obj_name=cutter_obj.name,
+                                         node_name="ObjectCutter",
-                                              cutter_type=self.cutter_type.capitalize())
+                                         node_label=name)
-
-        return {'FINISHED'}
-
-
-class ObjectCutter(bpy.types.Operator, AddCustomNode):
-    bl_idname = "bioxelnodes.object_cutter"
-    bl_label = "Object Cutter"
-    bl_description = "Object Cutter"
-    bl_icon = "NODE"
-    bl_options = {'UNDO'}
-
-    cutter_obj_name: bpy.props.StringProperty()  # type: ignore
-
-    cutter_type: bpy.props.StringProperty()  # type: ignore
-
-    def execute(self, context):
-        cutter_obj = bpy.data.objects.get(self.cutter_obj_name)
-        if cutter_obj == None:
-            self.report({"WARNING"}, "Get no layer.")
-            return {'FINISHED'}
-
-        self.get_node_tree(self.node_type, self.node_link)
-        prev_context = bpy.context.area.type
-        bpy.context.area.type = 'NODE_EDITOR'
-        bpy.ops.node.add_node('INVOKE_DEFAULT',
-                              type='GeometryNodeGroup',
-                              use_transform=True)
-        bpy.context.area.type = prev_context
             node = bpy.context.active_node
-
+            node.inputs[0].default_value = name
-        self.assign_node_tree(node)
-        node.show_options = False
-
-        node.label = "Object Cutter"
-        node.inputs[0].default_value = self.cutter_type
             node.inputs[1].default_value = cutter_obj
 
-        return {"FINISHED"}
+        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        self.nodes_file = custom_nodes.nodes_file
-        self.node_type = "BioxelNodes_ObjectCutter"
-        return self.execute(context)
 
 
 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"
     bl_icon = "MESH_PLANE"
     cutter_type = "plane"
 
@@ -308,7 +292,7 @@ class AddPlaneCutter(bpy.types.Operator, AddCutter):
 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"
     bl_icon = "MESH_CYLINDER"
     cutter_type = "cylinder"
 
@@ -316,7 +300,7 @@ class AddCylinderCutter(bpy.types.Operator, AddCutter):
 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"
     bl_icon = "MESH_CUBE"
     cutter_type = "cube"
 
@@ -324,7 +308,7 @@ class AddCubeCutter(bpy.types.Operator, AddCutter):
 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"
     bl_icon = "MESH_UVSPHERE"
     cutter_type = "sphere"
 
@@ -332,15 +316,128 @@ class AddSphereCutter(bpy.types.Operator, AddCutter):
 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"
     bl_icon = "MESH_CONE"
     cutter_type = "pie"
 
 
-class ScaleContainer(bpy.types.Operator):
+class AddSlicer(bpy.types.Operator):
-    bl_idname = "bioxelnodes.scale_container"
+    bl_idname = "bioxelnodes.add_slicer"
-    bl_label = "Scale Container"
+    bl_label = "Add a Slicer"
-    bl_description = "Scale Container."
+    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,
+                                       get_use_link())
+
+        slice_node.inputs[1].default_value = slicer_obj
+
+        output_node = get_nodes_by_type(node_group,
+                                        'NodeGroupOutput')[0]
+        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,
+                                        get_use_link())
+
+        parent_node.inputs[1].default_value = locator_obj
+
+        output_node = get_nodes_by_type(node_group,
+                                        'NodeGroupOutput')[0]
+        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",
@@ -348,6 +445,11 @@ class ScaleContainer(bpy.types.Operator):
                                          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)
 
@@ -358,10 +460,12 @@ class ScaleContainer(bpy.types.Operator):
         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):
-            bioxel_size = get_layer_prop_value(layer_obj, "bioxel_size")
+            layer_obj.data.render.space = 'WORLD'
-            layer_obj.data.render.step_size = self.scene_scale * bioxel_size
+            layer_obj.data.render.step_size = self.scene_scale * self.step_size
 
         return {'FINISHED'}
 
@@ -371,49 +475,51 @@ class ScaleContainer(bpy.types.Operator):
         if container_obj is None:
             return self.execute(context)
         else:
-            self.scene_scale = container_obj.scale[0]
+            self.scene_scale = container_obj.get("scene_scale") or 0.01
-            context.window_manager.invoke_props_dialog(self,
+            self.step_size = container_obj.get("step_size") or 1
-                                                       width=500)
+            context.window_manager.invoke_props_dialog(self)
             return {'RUNNING_MODAL'}
 
 
-class SaveAllLayerCaches(bpy.types.Operator):
+def get_container_layers(context, layer_filter=None):
-    bl_idname = "bioxelnodes.save_all_layer_caches"
+    def _layer_filter(layer_obj, context):
-    bl_label = "Save All Layer Caches"
+        return True
-    bl_description = "Save Container's caches to directory."
+
+    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"
 
-    cache_dir: bpy.props.StringProperty(
+    success_msg = "Successfully saved all container layers."
-        name="Cache Directory",
-        subtype='DIR_PATH',
-        default="//"
-    )  # type: ignore
 
-    def execute(self, context):
+    def get_layers(self, context):
-        container_obj = get_container_obj(context.object)
+        def is_not_missing(layer_obj, context):
+            return not is_missing_layer(layer_obj)
+        return get_container_layers(context, is_not_missing)
 
-        if container_obj is None:
-            self.report({"WARNING"}, "Cannot find any bioxel container.")
-            return {'FINISHED'}
 
-        fails = []
+class RemoveContainerMissingLayers(bpy.types.Operator, RemoveLayers):
-        for layer_obj in get_container_layer_objs(container_obj):
+    bl_idname = "bioxelnodes.remove_container_missing_layers"
-            try:
+    bl_label = "Remove Container Missing Layers"
-                bpy.ops.bioxelnodes.save_layer_cache('EXEC_DEFAULT',
+    bl_description = "Remove all current container missing layers"
-                                                     layer_obj_name=layer_obj.name,
+    bl_icon = "BRUSH_DATA"
-                                                     cache_dir=self.cache_dir)
-            except:
-                fails.append(layer_obj)
 
-        if len(fails) == 0:
+    success_msg = "Successfully removed all container missing layers."
-            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 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_props_dialog(self,
+        context.window_manager.invoke_confirm(self,
-                                                   width=500)
+                                              event,
+                                              message=f"Are you sure to remove all **Missing** layers?")
         return {'RUNNING_MODAL'}

bioxelnodes/operators/io.py

@@ -7,9 +7,8 @@ from pathlib import Path
 
 from ..exceptions import CancelledByUser
 from ..props import BIOXELNODES_Series
-from ..bioxelutils.utils import (get_all_layer_objs, get_container_obj,
+from ..bioxelutils.common import (get_all_layer_objs, get_container_obj,
-                                 get_layer_obj,
+                                  get_layer_obj, is_incompatible)
-                                 get_container_objs_from_selection)
 from ..bioxelutils.container import (Container,
                                      add_layers,
                                      container_to_obj)
@@ -17,8 +16,9 @@ from ..bioxel.layer import Layer
 from ..bioxel.parse import (DICOM_EXTS, SUPPORT_EXTS,
                             get_ext, parse_volumetric_data)
 
-from .utils import (get_cache_dir,
+from ..utils import (get_cache_dir,
-                    progress_update, progress_bar, select_object)
+                     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()
@@ -83,7 +83,7 @@ class ImportAsScalar(bpy.types.Operator, ImportVolumetricData):
     bl_label = "Import as Scalar"
     bl_description = "Import Volumetric Data to Container as Scalar"
     bl_icon = "EVENT_S"
-    read_as = "scalar"
+    read_as = "SCALAR"
 
 
 class ImportAsLabel(bpy.types.Operator, ImportVolumetricData):
@@ -91,7 +91,7 @@ class ImportAsLabel(bpy.types.Operator, ImportVolumetricData):
     bl_label = "Import as Label"
     bl_description = "Import Volumetric Data to Container as Label"
     bl_icon = "EVENT_L"
-    read_as = "label"
+    read_as = "LABEL"
 
 
 class ImportAsColor(bpy.types.Operator, ImportVolumetricData):
@@ -99,7 +99,7 @@ class ImportAsColor(bpy.types.Operator, ImportVolumetricData):
     bl_label = "Import as Label"
     bl_description = "Import Volumetric Data to Container as Label"
     bl_icon = "EVENT_C"
-    read_as = "color"
+    read_as = "COLOR"
 
 
 class BIOXELNODES_FH_ImportVolumetricData(bpy.types.FileHandler):
@@ -142,6 +142,8 @@ class ParseVolumetricData(bpy.types.Operator):
     bl_options = {'UNDO'}
 
     meta = None
+    label_count = 0
+    dtype = None
     thread = None
     _timer = None
 
@@ -160,10 +162,10 @@ class ParseVolumetricData(bpy.types.Operator):
                                                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", ""),
+                                           ("LABEL", "Labels", ""),
-                                           ("color", "Color", "")])  # type: ignore
+                                           ("COLOR", "Color", "")])  # type: ignore
 
     series_id: bpy.props.EnumProperty(name="Select Series",
                                       items=get_series_ids)  # type: ignore
@@ -172,6 +174,11 @@ 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'}
@@ -205,6 +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
@@ -270,25 +279,48 @@ 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'}
+
         orig_shape = self.meta['xyz_shape']
         orig_spacing = self.meta['spacing']
-        if orig_spacing[2] == 1 and orig_spacing[0] < 0.1:
+
-            spacing_log10 = math.floor(math.log10(min(*orig_spacing)))
+        min_log10 = math.floor(math.log10(min(*orig_spacing)))
-            orig_spacing = (orig_spacing[0] * math.pow(10, -spacing_log10-1),
+        max_log10 = math.floor(math.log10(max(*orig_spacing)))
-                            orig_spacing[1] * math.pow(10, -spacing_log10-1),
+        # 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))
 
-        min_size = min(orig_spacing[0],
+        bioxel_size = max(min(*orig_spacing), 1.0)
-                       orig_spacing[1], orig_spacing[2])
-        bioxel_size = max(min_size, 1.0)
 
-        # layer_shape = get_layer_shape(1, orig_shape, orig_spacing)
+        layer_shape = get_layer_shape(bioxel_size,
-        # layer_size = get_layer_size(layer_shape,
+                                      orig_shape,
-        #                             bioxel_size)
+                                      orig_spacing)
-        # log10 = math.floor(math.log10(max(*layer_size)))
+        layer_size = get_layer_size(layer_shape,
-        # log10 = max(1, log10)
+                                    bioxel_size,
-        # log10 = min(3, log10)
+                                    0.01)
-        # scene_scale = math.pow(10, -log10)
+        min_log10 = math.floor(math.log10(min(*layer_size)))
+        max_log10 = math.floor(math.log10(max(*layer_size)))
+
+        if min_log10 > 0:
+            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":
@@ -313,6 +345,7 @@ class ParseVolumetricData(bpy.types.Operator):
             channel_count=self.meta['channel_count'],
             container_obj_name=container_obj_name,
             read_as=self.read_as,
+            label_count=self.label_count,
             scene_scale=scene_scale
         )
 
@@ -320,6 +353,8 @@ class ParseVolumetricData(bpy.types.Operator):
         return {'FINISHED'}
 
     def invoke(self, context, event):
+        # 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'}
@@ -420,17 +455,17 @@ 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
 
@@ -460,11 +495,13 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
 
     channel_count: bpy.props.IntProperty()  # type: ignore
 
+    label_count: bpy.props.IntProperty()  # type: ignore
+
     read_as: bpy.props.EnumProperty(name="Read as",
-                                    default="scalar",
+                                    default="SCALAR",
-                                    items=[("scalar", "Scalar", ""),
+                                    items=[("SCALAR", "Scalar", ""),
-                                           ("label", "Labels", ""),
+                                           ("LABEL", "Labels", ""),
-                                           ("color", "Color", "")])  # type: ignore
+                                           ("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,
@@ -482,11 +519,14 @@ 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):
@@ -516,26 +556,26 @@ 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)
@@ -551,6 +591,7 @@ 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 = []
@@ -590,11 +631,13 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
                         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
@@ -605,8 +648,6 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
                         # If all values are the same, the normalized array will be all zeros
                         data = np.zeros_like(data, dtype=np.float32)
 
-                    # Convert the normalized array to float dtype
-                    data = data.astype(np.float32)
                 else:
                     data = data.astype(np.float32)
 
@@ -650,7 +691,21 @@ 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):
@@ -767,15 +822,17 @@ 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:
             name = self.container_name or "Container"
             container = Container(name=name,
                                   layers=self.layers)
 
+            step_size = container.layers[0].bioxel_size[0]*5
             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)
 
@@ -806,55 +863,70 @@ 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")
+
+        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

@@ -1,19 +1,16 @@
 from pathlib import Path
 import bpy
-import re
 
 import numpy as np
 
+from ..exceptions import NoContent
 from ..bioxel.layer import Layer
-from ..utils import copy_to_dir
+from ..bioxelutils.common import (get_container_obj, get_layer_kind, get_layer_label, get_layer_name,
-from ..customnodes.nodes import AddCustomNode
-from ..bioxelutils.utils import (get_container_obj,
                                   get_layer_prop_value,
                                   get_container_layer_objs,
-                                 get_node_type, set_layer_prop_value)
+                                  get_node_type, is_missing_layer, set_layer_prop_value)
 from ..bioxelutils.layer import layer_to_obj, obj_to_layer
-from .utils import get_cache_dir, get_layer_item_label, get_layer_label, get_preferences
+from ..utils import get_cache_dir, copy_to_dir
-from ..nodes import custom_nodes
 
 
 def get_label_layer_selection(self, context):
@@ -21,134 +18,244 @@ 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
 
 
-def get_selected_objs_in_node_tree(context):
+class FetchLayer(bpy.types.Operator):
-    select_objs = []
+    bl_idname = "bioxelnodes.fetch_layer"
-    # node_group = context.space_data.edit_tree
+    bl_label = "Fetch Layer"
-    for node in context.selected_nodes:
+    bl_description = "Fetch layer from current container"
-        if get_node_type(node) == "BioxelNodes_FetchLayer":
+    bl_icon = "NODE"
-            layer_obj = node.inputs[0].default_value
-            if layer_obj != None:
-                cache_filepath = Path(bpy.path.abspath(
-                    layer_obj.data.filepath)).resolve()
-                if cache_filepath.is_file():
-                    select_objs.append(layer_obj)
-    return select_objs
-
-
-class LayerOperator():
     bl_options = {'UNDO'}
+
     layer_obj_name: bpy.props.StringProperty(
         options={"HIDDEN"})  # type: ignore
 
+    @classmethod
+    def description(cls, context, properties):
+        layer_obj_name = properties.layer_obj_name
+        layer_obj = bpy.data.objects.get(layer_obj_name)
+        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
     def layer_obj(self):
         return bpy.data.objects.get(self.layer_obj_name)
 
-    @property
-    def is_lost(self):
-        if self.layer_obj is None:
-            return None
-
-        cache_filepath = Path(bpy.path.abspath(
-            self.layer_obj.data.filepath)).resolve()
-        return not cache_filepath.is_file()
-
-
-class FetchLayer(bpy.types.Operator, LayerOperator, AddCustomNode):
-    bl_idname = "bioxelnodes.fetch_layer"
-    bl_label = "Fetch Layer"
-    bl_description = "Fetch Layer"
-    bl_icon = "NODE"
-
     def execute(self, context):
         if self.layer_obj == None:
             self.report({"WARNING"}, "Get no layer.")
             return {'FINISHED'}
 
-        if self.is_lost:
+        if is_missing_layer(self.layer_obj):
             self.report({"WARNING"}, "Selected layer is lost.")
             return {'FINISHED'}
 
-        self.get_node_tree(self.node_type, self.node_link)
+        bpy.ops.bioxelnodes.add_node('EXEC_DEFAULT',
-        prev_context = bpy.context.area.type
+                                     node_name="FetchLayer",
-        bpy.context.area.type = 'NODE_EDITOR'
+                                     node_label="Fetch Layer")
-        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.inputs[0].default_value = self.layer_obj
-        node.show_options = False
+        node.label = get_layer_label(self.layer_obj)
-        layer_obj = self.layer_obj
-        node.inputs[0].default_value = layer_obj
-        node.label = get_layer_label(layer_obj)
 
         return {"FINISHED"}
 
-    def invoke(self, context, event):
+
-        self.nodes_file = custom_nodes.nodes_file
+def get_selected_layers(context, layer_filter=None):
-        self.node_type = "BioxelNodes_FetchLayer"
+    def _layer_filter(layer_obj, context):
-        return self.execute(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))
 
 
-class FetchLayerMenu(bpy.types.Menu):
+def get_selected_layer(context, layer_filter=None):
-    bl_idname = "BIOXELNODES_MT_ADD_LAYER"
+    layer_objs = get_selected_layers(context, layer_filter)
-    bl_label = "Fetch Layer"
+    return layer_objs[0] if len(layer_objs) > 0 else None
-
-    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_item_label(context, layer_obj))
-            op.layer_obj_name = layer_obj.name
 
 
-class ModifyLayerOperator(LayerOperator):
+class OutputLayerOperator():
-    def layer_operate(self, orig_layer: Layer):
+    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):
         layer_obj = layer_to_obj(layer,
-                                 container_obj=self.layer_obj.parent,
+                                 container_obj=context.object,
-                                 cache_dir=get_cache_dir(context))
+                                 cache_dir=get_cache_dir())
 
         bpy.ops.bioxelnodes.fetch_layer('INVOKE_DEFAULT',
                                         layer_obj_name=layer_obj.name)
 
     def execute(self, context):
-        if self.layer_obj == None:
+        layer_obj = get_selected_layer(context)
+        if layer_obj == None:
             self.report({"WARNING"}, "Get no layer.")
             return {'FINISHED'}
 
-        if self.is_lost:
+        if is_missing_layer(layer_obj):
             self.report({"WARNING"}, "Selected layer is lost.")
             return {'FINISHED'}
 
-        orig_layer = obj_to_layer(self.layer_obj)
+        orig_layer = obj_to_layer(layer_obj)
-        new_layer = self.layer_operate(orig_layer)
+        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 ResampleScalar(bpy.types.Operator, ModifyLayerOperator):
+class LayerOperator():
-    bl_idname = "bioxelnodes.resample_scalar"
+
-    bl_label = "Resample Scalar"
+    def operate(self, layer_obj: bpy.types.Object, context):
-    bl_description = "Resample Scalar"
+        """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):
+        layer_obj = get_selected_layer(context)
+        if layer_obj:
+            self.frame_duration = layer_obj.data.frame_duration
+            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 RelocateLayer(bpy.types.Operator, LayerOperator):
+    bl_idname = "bioxelnodes.relocate_layer"
+    bl_label = "Relocate Layer Cache"
+    bl_description = "Relocate layer cache"
+    bl_icon = "FILE"
+
+    filepath: bpy.props.StringProperty(subtype="FILE_PATH")  # type: ignore
+
+    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 Iteration",
+                                  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,
@@ -161,19 +268,21 @@ class ResampleScalar(bpy.types.Operator, ModifyLayerOperator):
                 int(orig_shape[1]*orig_size/new_size),
                 int(orig_shape[2]*orig_size/new_size))
 
-    def layer_operate(self, orig_layer: Layer):
+    def operate(self, orig_layer: Layer, context):
-        modified_layer = orig_layer.copy()
+        new_layer = orig_layer.copy()
-        new_shape = self.get_new_shape(modified_layer.shape,
+        new_shape = self.get_new_shape(new_layer.shape,
-                                       modified_layer.bioxel_size[0],
+                                       new_layer.bioxel_size[0],
                                        self.bioxel_size)
 
-        modified_layer.resize(new_shape)
+        new_layer.resize(new_shape, self.smooth)
-        modified_layer.name = f"{orig_layer.name}_R-{self.bioxel_size:.2f}"
+        new_layer.name = self.new_layer_name \
-        return modified_layer
+            or f"{orig_layer.name}_R-{self.bioxel_size:.2f}"
+        return new_layer
 
     def draw(self, context):
-        orig_shape = get_layer_prop_value(self.layer_obj, "shape")
+        layer_obj = get_selected_layer(context)
-        orig_size = get_layer_prop_value(self.layer_obj, "bioxel_size")
+        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)
@@ -186,45 +295,49 @@ class ResampleScalar(bpy.types.Operator, ModifyLayerOperator):
             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):
-        if self.layer_obj:
+        layer_obj = get_selected_layer(context)
-            bioxel_size = get_layer_prop_value(self.layer_obj, "bioxel_size")
+        if layer_obj:
-
+            name = get_layer_label(layer_obj)
-            self.bioxel_size = bioxel_size
+            self.bioxel_size = get_layer_prop_value(layer_obj,
+                                                    "bioxel_size")
             context.window_manager.invoke_props_dialog(self,
-                                                       width=400,
+                                                       title=f"Resample {name}")
-                                                       title=f"Resample {self.layer_obj.name}")
             return {'RUNNING_MODAL'}
         else:
             return self.execute(context)
 
 
-class SignScalar(bpy.types.Operator, ModifyLayerOperator):
+class SignScalar(bpy.types.Operator, OutputLayerOperator):
     bl_idname = "bioxelnodes.sign_scalar"
-    bl_label = "Sign Scalar"
+    bl_label = "Sign Value"
-    bl_description = "Sign the scalar value"
+    bl_description = "Sign value"
     bl_icon = "REMOVE"
 
-    def layer_operate(self, orig_layer: Layer):
+    def operate(self, orig_layer: Layer, context):
-        modified_layer = orig_layer.copy()
+        new_layer = orig_layer.copy()
-        modified_layer.data = -orig_layer.data
+        new_layer.data = -orig_layer.data
-        modified_layer.name = f"{orig_layer.name}_Sign"
+        new_layer.name = self.new_layer_name \
-        return modified_layer
+            or f"{orig_layer.name}_Sign"
+        return new_layer
 
     def invoke(self, context, event):
-        if self.layer_obj:
+        layer_obj = get_selected_layer(context)
-            context.window_manager.invoke_confirm(self,
+        if layer_obj:
-                                                  event,
+            name = get_layer_label(layer_obj)
-                                                  message=f"Are you sure to sign {self.layer_obj.name}?")
+            context.window_manager.invoke_props_dialog(self,
+                                                       title=f"Sign {name}")
             return {'RUNNING_MODAL'}
         else:
             return self.execute(context)
 
 
-class FillOperator(ModifyLayerOperator):
+class FillOperator(OutputLayerOperator):
 
     fill_value: bpy.props.FloatProperty(
         name="Fill Value",
@@ -238,13 +351,13 @@ class FillOperator(ModifyLayerOperator):
     )  # type: ignore
 
     def invoke(self, context, event):
-        if self.layer_obj:
+        layer_obj = get_selected_layer(context)
-            scalar_min = get_layer_prop_value(self.layer_obj, "min")
+        if layer_obj:
-
+            scalar_min = get_layer_prop_value(layer_obj, "min")
             self.fill_value = min(scalar_min, 0)
+            name = get_layer_label(layer_obj)
             context.window_manager.invoke_props_dialog(self,
-                                                       width=400,
+                                                       title=f"Fill {name}")
-                                                       title=f"Fill {self.layer_obj.name}")
             return {'RUNNING_MODAL'}
         else:
             return self.execute(context)
@@ -253,7 +366,7 @@ class FillOperator(ModifyLayerOperator):
 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_description = "Fill value by threshold"
     bl_icon = "EMPTY_SINGLE_ARROW"
 
     threshold: bpy.props.FloatProperty(
@@ -262,21 +375,22 @@ class FillByThreshold(bpy.types.Operator, FillOperator):
         default=128,
     )  # type: ignore
 
-    def layer_operate(self, orig_layer: Layer):
+    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 = orig_layer.copy()
+        new_layer = orig_layer.copy()
-        modified_layer.fill(self.fill_value, mask)
+        new_layer.fill(self.fill_value, mask, 3)
-        modified_layer.name = f"{orig_layer.name}_F-{self.threshold}"
+        new_layer.name = self.new_layer_name \
-        return modified_layer
+            or f"{orig_layer.name}_F-{self.threshold:.2f}"
+        return new_layer
 
 
 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(
@@ -291,82 +405,112 @@ class FillByRange(bpy.types.Operator, FillOperator):
         default=256,
     )  # type: ignore
 
-    def layer_operate(self, orig_layer: Layer):
+    def operate(self, orig_layer: Layer, context):
         data = np.amax(orig_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 = orig_layer.copy()
+        new_layer = orig_layer.copy()
-        modified_layer.fill(self.fill_value, mask)
+        new_layer.fill(self.fill_value, mask, 3)
-        modified_layer.name = f"{orig_layer.name}_F-{self.from_min}-{self.from_max}"
+        new_layer.name = self.new_layer_name \
-        return modified_layer
+            or f"{orig_layer.name}_F-{self.from_min:.2f}-{self.from_max:.2f}"
+        return new_layer
 
 
 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"
 
+    smooth: bpy.props.IntProperty(name="Smooth Iteration",
+                                  default=0,
+                                  soft_min=0, soft_max=5,
+                                  options={"SKIP_SAVE"})  # type: ignore
+
     label_obj_name: bpy.props.EnumProperty(name="Label Layer",
                                            items=get_label_layer_selection)  # type: ignore
 
-    def layer_operate(self, orig_layer: Layer):
+    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'}
 
         label_layer = obj_to_layer(label_obj)
-        label_layer.resize(orig_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 = orig_layer.copy()
+        new_layer = orig_layer.copy()
-        modified_layer.fill(self.fill_value, mask)
+        new_layer.fill(self.fill_value, mask, 3)
-        modified_layer.name = f"{orig_layer.name}_F-{label_layer.name}"
+        new_layer.name = self.new_layer_name \
-        return modified_layer
+            or f"{orig_layer.name}_F-{label_layer.name}"
+        return new_layer
 
 
-class CombineLabels(bpy.types.Operator, ModifyLayerOperator):
+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 get_selected_objs_in_node_tree(context)
+        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:]
 
         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(
+            new_layer.data = np.maximum(
-                modified_layer.data, label_layer.data)
+                new_layer.data, label_layer.data)
             label_names.append(label_layer.name)
 
-        modified_layer.name = f"C-{'-'.join(label_names)}"
+        new_layer.name = self.new_layer_name \
+            or f"C-{'-'.join(label_names)}"
 
-        self.add_layer_node(context, modified_layer)
+        self.add_layer_node(context, new_layer)
         return {'FINISHED'}
 
 
-class SaveLayerCache(bpy.types.Operator, LayerOperator):
+class BatchLayerOperator():
-    bl_idname = "bioxelnodes.save_layer_cache"
+    success_msg = "Successfully done selected layers."
-    bl_label = "Save Layer Cache"
+    fail_msg = "fails."
-    bl_description = "Save Layer Cache"
+
-    bl_icon = "FILE_TICK"
+    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",
@@ -374,23 +518,14 @@ class SaveLayerCache(bpy.types.Operator, LayerOperator):
         default="//"
     )  # type: ignore
 
-    def execute(self, context):
+    def operate(self, layer_obj, context):
-        if self.layer_obj == None:
-            self.report({"WARNING"}, "Get no layer.")
-            return {'FINISHED'}
-
-        if self.is_lost:
-            self.report({"WARNING"}, "Selected layer is lost.")
-            return {'FINISHED'}
-
-        # "//"
         output_dir = bpy.path.abspath(self.cache_dir)
-        source_dir = bpy.path.abspath(self.layer_obj.data.filepath)
+        source_dir = bpy.path.abspath(layer_obj.data.filepath)
 
         source_path: Path = Path(source_dir).resolve()
-        is_sequence = self.layer_obj.data.is_sequence
+        is_sequence = layer_obj.data.is_sequence
 
-        name = self.layer_obj.name if is_sequence else f"{self.layer_obj.name}.vdb"
+        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()
 
@@ -401,124 +536,69 @@ class SaveLayerCache(bpy.types.Operator, LayerOperator):
 
         blend_path = Path(bpy.path.abspath("//")).resolve()
 
-        self.layer_obj.data.filepath = bpy.path.relpath(str(output_path),
+        layer_obj.data.filepath = bpy.path.relpath(str(output_path),
                                                    start=str(blend_path))
 
         return {'FINISHED'}
 
     def invoke(self, context, event):
-        if self.layer_obj:
+        context.window_manager.invoke_props_dialog(self)
-            context.window_manager.invoke_props_dialog(self,
-                                                       width=500)
         return {'RUNNING_MODAL'}
-        else:
-            return self.execute(context)
 
 
-class RenameLayer(bpy.types.Operator, LayerOperator):
+class RemoveLayers(BatchLayerOperator):
-    bl_idname = "bioxelnodes.rename_layer"
+    fail_msg = "fail to remove."
-    bl_label = "Rename Layer"
-    bl_description = "Rename Layer"
-    bl_icon = "FILE_FONT"
 
-    name: bpy.props.StringProperty(name="New Name")  # type: ignore
+    def operate(self, layer_obj, context):
-
+        for node_group in bpy.data.node_groups:
-    def execute(self, context):
-        if self.layer_obj == None:
-            self.report({"WARNING"}, "Get no layer.")
-            return {'FINISHED'}
-
-        if self.is_lost:
-            self.report({"WARNING"}, "Selected layer is lost.")
-            return {'FINISHED'}
-
-        name = f"{self.layer_obj.parent.name}_{self.name}"
-        self.layer_obj.name = name
-        self.layer_obj_name = name
-        self.layer_obj.data.name = name
-
-        set_layer_prop_value(self.layer_obj, "name", self.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 == self.layer_obj:
+                    if node.inputs[0].default_value == layer_obj:
-                    node.label = self.name
-
-        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        if self.layer_obj:
-            self.name = get_layer_prop_value(self.layer_obj, "name")
-            context.window_manager.invoke_props_dialog(self,
-                                                       width=500,
-                                                       title=f"rename {self.layer_obj.name}")
-            return {'RUNNING_MODAL'}
-        else:
-            return self.execute(context)
-
-
-class RemoveLayer(bpy.types.Operator, LayerOperator):
-    bl_idname = "bioxelnodes.remove_layer"
-    bl_label = "Remove Selected Layer"
-    bl_description = "Remove Layer"
-    bl_icon = "TRASH"
-
-    def execute(self, context):
-        if self.layer_obj == None:
-            self.report({"WARNING"}, "Get no layer.")
-            return {'FINISHED'}
-
-        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 == self.layer_obj:
                         node_group.nodes.remove(node)
 
         cache_filepath = Path(bpy.path.abspath(
-            self.layer_obj.data.filepath)).resolve()
+            layer_obj.data.filepath)).resolve()
 
         if cache_filepath.is_file():
-            if self.layer_obj.data.is_sequence:
+            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(self.layer_obj.data)
+        bpy.data.volumes.remove(layer_obj.data)
 
         return {'FINISHED'}
 
-    def invoke(self, context, event):
-        if self.layer_obj:
-            context.window_manager.invoke_confirm(self,
-                                                  event,
-                                                  message=f"Are you sure to remove {self.layer_obj.name}?")
-            return {'RUNNING_MODAL'}
-        else:
-            return self.execute(context)
-
-
-class RemoveMissingLayers(bpy.types.Operator):
-    bl_idname = "bioxelnodes.remove_lost_layers"
-    bl_label = "Remove All Missing Layers"
-    bl_description = "Remove all missing "
-    bl_icon = "BRUSH_DATA"
-
-    def execute(self, context):
-        container_obj = context.object
-        for layer_obj in get_container_layer_objs(container_obj):
-            cache_filepath = Path(bpy.path.abspath(
-                layer_obj.data.filepath)).resolve()
-            if cache_filepath.is_file():
-                continue
-            bpy.ops.bioxelnodes.remove_layer('EXEC_DEFAULT',
-                                             layer_obj_name=layer_obj.name)
-        return {'FINISHED'}
-
     def invoke(self, context, event):
         context.window_manager.invoke_confirm(self,
                                               event,
-                                              message=f"Are you sure to remove all **Missing** layers?")
+                                              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

@@ -1,54 +1,51 @@
 import bpy
 from pathlib import Path
 import shutil
-from .utils import get_cache_dir
-from ..nodes import custom_nodes
-from ..bioxelutils.utils import (get_container_objs_from_selection,
-                                 get_all_layer_objs,
-                                 get_container_layer_objs)
 
-CLASS_PREFIX = "BIOXELNODES_MT_NODES"
+from ..bioxelutils.common import get_all_layer_objs, is_missing_layer, set_file_prop
+from .layer import RemoveLayers, SaveLayersCache
+
+from ..constants import NODE_LIB_FILEPATH, VERSION
+from ..utils import get_cache_dir
 
 
-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'}
+
+    node_lib_filename: bpy.props.StringProperty(
+        default=""
+    )  # type: ignore
 
     def execute(self, context):
-        file_name = Path(custom_nodes.nodes_file).name
+        lib_filepath = Path(NODE_LIB_FILEPATH.parent,
-        for lib in bpy.data.libraries:
+                            f"{self.node_lib_filename}.blend")
-            lib_path = Path(bpy.path.abspath(lib.filepath)).resolve()
+        node_libs = []
-            lib_name = lib_path.name
+        for node_group in bpy.data.node_groups:
-            if lib_name == file_name:
+            if node_group.name.startswith("BioxelNodes"):
-                if str(lib_path) != custom_nodes.nodes_file:
+                node_lib = node_group.library
-                    lib.filepath = custom_nodes.nodes_file
+                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_filepath)
+            # FIXME: may cause crash
+            node_lib.reload()
 
         self.report({"INFO"}, f"Successfully relinked.")
 
         return {'FINISHED'}
 
 
-class SaveStagedData(bpy.types.Operator):
+class SaveNodeLib(bpy.types.Operator):
-    bl_idname = "bioxelnodes.save_staged_data"
+    bl_idname = "bioxelnodes.save_node_lib"
-    bl_label = "Save Staged Data"
+    bl_label = "Save Node Library"
-    bl_description = "Save all staged data in this file for sharing"
+    bl_description = "Save node library file to local"
-
+    bl_options = {'UNDO'}
-    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",
@@ -57,98 +54,66 @@ class SaveStagedData(bpy.types.Operator):
     )  # type: ignore
 
     def execute(self, context):
-        if self.save_lib:
-            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:
-                file_name = Path(file).name
-                # "//"
         lib_dir = bpy.path.abspath(self.lib_dir)
-
+        local_lib_path: Path = Path(lib_dir, NODE_LIB_FILEPATH.name).resolve()
-                output_path: Path = Path(lib_dir, file_name).resolve()
+        addon_lib_path: Path = NODE_LIB_FILEPATH
-                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 local_lib_path != addon_lib_path:
+            shutil.copy(addon_lib_path, local_lib_path)
 
-        if self.save_cache:
+        libs = []
-            fails = []
+        for node_group in bpy.data.node_groups:
-            for layer_obj in get_all_layer_objs():
+            if node_group.name.startswith("BioxelNodes"):
-                try:
+                if node_group.library:
-                    bpy.ops.bioxelnodes.save_layer_cache('EXEC_DEFAULT',
+                    libs.append(node_group.library)
-                                                         layer_obj_name=layer_obj.name,
-                                                         cache_dir=self.cache_dir)
-                except:
-                    fails.append(layer_obj)
 
-            if len(fails) == 0:
+        libs = list(set(libs))
-                self.report({"INFO"}, f"Successfully saved bioxel layers.")
+        for lib in libs:
-            else:
+            lib.filepath = bpy.path.relpath(str(local_lib_path),
-                self.report(
+                                            start=str(blend_path))
-                    {"WARNING"}, f"{','.join([layer_obj.name for layer_obj in fails])} fail to save.")
+
+        set_file_prop("addon_version", VERSION)
 
         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 CleanAllCaches(bpy.types.Operator):
+    bl_idname = "bioxelnodes.clear_temp"
-    bl_idname = "bioxelnodes.clear_all_caches"
+    bl_label = "Clean Temp"
-    bl_label = "Clean All Caches in Temp"
+    bl_description = "Clean all cache in temp (include other project cache)"
-    bl_description = "Clean all caches saved in temp"
 
     def execute(self, context):
-        cache_dir = get_cache_dir(context)
+        cache_dir = get_cache_dir()
         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 Preset"
+    bl_label = "Render Setting Presets"
-    bl_description = "Render Setting Preset"
+    bl_description = "Render setting presets for bioxel"
+    bl_options = {'UNDO'}
 
     PRESETS = {
         "preview_e": "Preview (EEVEE)",
@@ -190,21 +155,24 @@ class RenderSettingPreset(bpy.types.Operator):
             bpy.context.scene.cycles.transparent_max_bounces = 16
             bpy.context.scene.cycles.volume_preview_step_rate = 1
             bpy.context.scene.cycles.volume_step_rate = 1
+            # bpy.context.scene.cycles.use_fast_gi = True
 
         elif self.preset == "production_c":
             bpy.context.scene.render.engine = 'CYCLES'
             bpy.context.scene.cycles.shading_system = True
             bpy.context.scene.cycles.volume_bounces = 16
             bpy.context.scene.cycles.transparent_max_bounces = 32
-            bpy.context.scene.cycles.volume_preview_step_rate = 0.1
+            bpy.context.scene.cycles.volume_preview_step_rate = 0.5
-            bpy.context.scene.cycles.volume_step_rate = 0.1
+            bpy.context.scene.cycles.volume_step_rate = 0.5
+            # bpy.context.scene.cycles.use_fast_gi = False
 
         return {'FINISHED'}
 
+
 class SliceViewer(bpy.types.Operator):
     bl_idname = "bioxelnodes.slice_viewer"
     bl_label = "Slice Viewer"
-    bl_description = "Slice Viewer"
+    bl_description = "A preview scene setting for viewing slicers"
     bl_icon = "FILE_VOLUME"
 
     def execute(self, context):
@@ -224,5 +192,47 @@ class SliceViewer(bpy.types.Operator):
                 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'}

bioxelnodes/operators/node.py

@@ -0,0 +1,62 @@
+import bpy
+
+from ..bioxelutils.common import get_file_prop, is_incompatible, local_lib_not_updated
+from ..constants import VERSION
+from ast import literal_eval
+from ..bioxelutils.node import assign_node_group, get_node_group
+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'}
+
+        get_node_group(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_group(node, self.node_type)
+        node.label = self.node_label
+
+        node.show_options = False
+
+        if local_lib_not_updated():
+            self.report({"WARNING"},
+                        "Local 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 ..bioxelutils.utils import get_layer_prop_value
-from .. import __package__ as base_package
-
-
-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)
-
-
-def get_layer_item_label(context, layer_obj):
-    label = get_layer_label(layer_obj)
-    cache_filepath = Path(bpy.path.abspath(layer_obj.data.filepath)).resolve()
-    if cache_filepath.is_file():
-        cache_dirpath = Path(get_cache_dir(context))
-        if cache_dirpath in cache_filepath.parents:
-            label = "* " + label
-
-    else:
-        label = "**MISSING**" + label
-
-    return label
-
-
-def get_layer_label(layer_obj):
-    name = get_layer_prop_value(layer_obj, "name")
-    kind = get_layer_prop_value(layer_obj, "kind")
-
-    return f"{name}"

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

@@ -1,6 +1,6 @@
 import bpy
 
-from .bioxelutils.utils import get_node_type
+from .bioxelutils.common import get_node_type
 
 
 class BIOXELNODES_UL_layer_list(bpy.types.UIList):
@@ -27,6 +27,8 @@ def select_layer(self, context):
                 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

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"

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "bioxelnodes"
-version = "0.4.0"
+version = "1.0.0"
 description = ""
 authors = ["Ma Nan <icrdr2010@outlook.com>"]
 license = "MIT"