Merge pull request #41 from OmooLab/feature/dev

Feature/dev

.gitignore

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

bioxelnodes/__init__.py

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

bioxelnodes/bioxel/layer.py

@@ -2,12 +2,10 @@ import copy
 import numpy as np
 
 from . import scipy
-from . import skimage as ski
 from . import scipy as ndi
 
 # 3rd-party
 import transforms3d
-
 # TODO: turn to dataclasses
 
 
@@ -71,23 +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(
-                    mask_frame.astype(np.float32), size=3)
+                if smooth > 0:
+                    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(
-                    mask_frame.astype(np.float32), size=3)
+                if smooth > 0:
+                    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,)
@@ -98,20 +100,19 @@ 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']:
-            data = np.amax(data, -1)
+        # # TXYZC > TXYZ
+        # if self.kind in ['label', 'scalar']:
+        #     data = np.amax(data, -1)
 
         # if self.kind in ['scalar']:
         #     dtype = data.dtype
-            # data = data.astype(np.float32)
+        # data = data.astype(np.float32)
 
         data_frames = ()
         for f in range(self.frame_count):
@@ -122,13 +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, :, :, :],
-                             zoom_factors,
+            order = 0 if frame.dtype == bool else 1
+            frame = ndi.zoom(frame,
+                             zoom_factors+[1.0],
+                             mode="nearest",
+                             grid_mode=False,
                              order=order)
-
+            if smooth > 0:
+                frame = frame.astype(self.dtype)
             data_frames += (frame,)
 
         data = np.stack(data_frames)
@@ -137,7 +147,10 @@ class Layer():
         #     data = data.astype(dtype)
 
         # TXYZ > TXYZC
-        if self.kind in ['label', 'scalar']:
-            data = np.expand_dims(data, axis=-1)  # expend channel
+        # if self.kind in ['label', 'scalar']:
+        #     data = np.expand_dims(data, axis=-1)  # expend channel
 
         self.data = data
+
+        mat_scale = transforms3d.zooms.zfdir2aff(factors[0])
+        self.affine = np.dot(self.affine, mat_scale)

bioxelnodes/bioxel/parse.py

@@ -1,6 +1,5 @@
 from pathlib import Path
 import numpy as np
-from .layer import Layer
 
 # 3rd-party
 import SimpleITK as sitk
@@ -42,7 +41,8 @@ DICOM_EXTS = ['', '.dcm', '.DCM', '.DICOM', '.ima', '.IMA']
 SEQUENCE_EXTS = ['.bmp', '.BMP',
                  '.jpg', '.JPG', '.jpeg', '.JPEG',
                  '.tif', '.TIF', '.tiff', '.TIFF',
-                 '.png', '.PNG']
+                 '.png', '.PNG',
+                 '.mrc']
 
 
 def get_ext(filepath: Path) -> str:
@@ -64,18 +64,40 @@ def get_ext(filepath: Path) -> str:
         return filepath.suffix
 
 
-def get_file_name(filepath: Path):
+def get_filename(filepath: Path):
     ext = get_ext(filepath)
-    return filepath.name.removesuffix(ext).replace(" ", "-")
+    return filepath.name.removesuffix(ext)
 
 
-def get_file_number(filepath: Path) -> str:
-    name = get_file_name(filepath)
+def get_filename_parts(filepath: Path) -> str:
+    def has_digits(s):
+        return any(char.isdigit() for char in s)
+
+    name = get_filename(filepath)
+    parts = name.replace(".", " ").replace("_", " ").split(" ")
+    skip_prefixs = ["CH", "ch", "channel"]
+    number_part = None
+    number_part_i = None
+
+    for i, part in enumerate(parts[::-1]):
+        if has_digits(part):
+            if not any([part.startswith(prefix) for prefix in skip_prefixs]):
+                number_part = part
+                number_part_i = len(parts)-i
+                break
+
+    if number_part is None:
+        return name, "", ""
+
+    prefix_parts = parts[:number_part_i-1]
+    prefix_parts_count = sum([len(part)+1 for part in prefix_parts])
+
     digits = ""
+    suffix = ""
 
     # Iterate through the characters in reverse order
     started = False
-    for char in name[::-1]:
+    for char in number_part[::-1]:
         if char.isdigit():
             started = True
             # If the character is a digit, add it to the digits string
@@ -84,20 +106,33 @@ def get_file_number(filepath: Path) -> str:
             if started:
                 # If a non-digit character is encountered, stop the loop
                 break
+            else:
+                suffix += char
+
+    digits = digits[::-1]
+
+    prefix_parts_count += len(number_part) - \
+        len(digits) - len(suffix)
 
     # Reverse the digits string to get the correct order
-    return digits[::-1]
+    prefix = name[:prefix_parts_count]
+    suffix = name[prefix_parts_count+len(digits):]
+
+    return prefix, digits, suffix
 
 
-def get_sequence_name(filepath: Path) -> str:
-    name = get_file_name(filepath)
-    number = get_file_number(filepath)
-    return name.removesuffix(number)
+def get_file_no_digits_name(filepath: Path) -> str:
+    prefix, digits, suffix = get_filename_parts(filepath)
+    prefix = remove_end_str(prefix, "_")
+    prefix = remove_end_str(prefix, ".")
+    prefix = remove_end_str(prefix, "-")
+    prefix = remove_end_str(prefix, " ")
+    return prefix + suffix
 
 
-def get_sequence_index(filepath: Path) -> int:
-    number = get_file_number(filepath)
-    return int(number) if number != "" else 0
+def get_file_index(filepath: Path) -> int:
+    prefix, digits, suffix = get_filename_parts(filepath)
+    return int(digits) if digits != "" else 0
 
 
 def collect_sequence(filepath: Path):
@@ -105,8 +140,8 @@ def collect_sequence(filepath: Path):
     for f in filepath.parent.iterdir():
         if f.is_file() \
                 and get_ext(filepath) == get_ext(f) \
-                and get_sequence_name(filepath) == get_sequence_name(f):
-            index = get_sequence_index(f)
+                and get_file_no_digits_name(filepath) == get_file_no_digits_name(f):
+            index = get_file_index(f)
             file_dict[index] = f
 
     # reomve isolated seq file
@@ -124,7 +159,13 @@ def collect_sequence(filepath: Path):
     return sequence
 
 
-def parse_volumetric_data(data_file: str, series_id="", progress_callback=None) -> Layer:
+def remove_end_str(string: str, end: str):
+    while string.endswith(end) and len(string) > 0:
+        string = string.removesuffix(end)
+    return string
+
+
+def parse_volumetric_data(data_file: str, series_id="", progress_callback=None):
     """Parse any volumetric data to numpy with shap (T,X,Y,Z,C)
 
     Args:
@@ -139,7 +180,7 @@ def parse_volumetric_data(data_file: str, series_id="", progress_callback=None)
     ext = get_ext(data_path)
 
     if progress_callback:
-        progress_callback(0, "Reading the Data...")
+        progress_callback(0.0, "Reading the Data...")
 
     is_sequence = False
     if ext in SEQUENCE_EXTS:
@@ -181,7 +222,7 @@ def parse_volumetric_data(data_file: str, series_id="", progress_callback=None)
             elif mrc.is_volume_stack():
                 data = np.expand_dims(data, axis=-1)  # expend channel
 
-            name = get_file_name(data_path)
+            name = get_file_no_digits_name(data_path)
             spacing = (mrc.voxel_size.x,
                        mrc.voxel_size.y,
                        mrc.voxel_size.z)
@@ -245,7 +286,7 @@ def parse_volumetric_data(data_file: str, series_id="", progress_callback=None)
             except:
                 ...
 
-            name = get_file_name(data_path)
+            name = get_file_no_digits_name(data_path)
         except:
             ...
 
@@ -297,10 +338,10 @@ def parse_volumetric_data(data_file: str, series_id="", progress_callback=None)
 
         elif ext in SEQUENCE_EXTS and is_sequence:
             itk_image = sitk.ReadImage(sequence)
-            name = get_sequence_name(data_path)
+            name = get_file_no_digits_name(data_path)
         else:
             itk_image = sitk.ReadImage(data_path)
-            name = get_file_name(data_path)
+            name = get_filename(data_path)
 
         # for key in itk_image.GetMetaDataKeys():
         #     print(f"{key},{itk_image.GetMetaData(key)}")

bioxelnodes/bioxelutils/common.py

@@ -0,0 +1,245 @@
+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]
+    node.location.y = target_node.location.y + offset[1]
+
+
+def move_node_between_nodes(node, target_nodes, offset=(0, 0)):
+    xs = []
+    ys = []
+    for target_node in target_nodes:
+        xs.append(target_node.location.x)
+        ys.append(target_node.location.y)
+
+    node.location.x = sum(xs) / len(xs) + offset[0]
+    node.location.y = sum(ys) / len(ys) + offset[1]
+
+
+def get_node_type(node):
+    node_type = type(node).__name__
+    if node_type == "GeometryNodeGroup":
+        node_type = node.node_tree.name
+
+    return node_type
+
+
+def get_nodes_by_type(node_group, type_name: str):
+    return [node for node in node_group.nodes if get_node_type(node) == type_name]
+
+
+def get_container_objs_from_selection():
+    container_objs = []
+    for obj in bpy.context.selected_objects:
+        if get_container_obj(obj):
+            container_objs.append(obj)
+
+    return list(set(container_objs))
+
+
+def get_container_obj(current_obj):
+    if current_obj:
+        if current_obj.get('bioxel_container'):
+            return current_obj
+        elif current_obj.get('bioxel_layer'):
+            parent = current_obj.parent
+            return parent if parent.get('bioxel_container') else None
+    return None
+
+
+def get_layer_prop_value(layer_obj: bpy.types.Object, prop_name: str):
+    node_group = layer_obj.modifiers[0].node_group
+    layer_node = get_nodes_by_type(node_group, "BioxelNodes__Layer")[0]
+    prop = layer_node.inputs.get(prop_name)
+    if prop is None:
+        return None
+
+    value = prop.default_value
+
+    if type(value).__name__ == "bpy_prop_array":
+        value = tuple(value)
+        return tuple([int(v) for v in value]) \
+            if prop in ["shape"] else value
+    elif type(value).__name__ == "str":
+        return str(value)
+    elif type(value).__name__ == "float":
+        value = float(value)
+        return round(value, 2) \
+            if prop in ["bioxel_size"] else value
+    elif type(value).__name__ == "int":
+        value = int(value)
+        return value
+    else:
+        return value
+
+
+def get_layer_name(layer_obj):
+    return get_layer_prop_value(layer_obj, "name")
+
+
+def get_layer_kind(layer_obj):
+    return get_layer_prop_value(layer_obj, "kind")
+
+
+def get_layer_label(layer_obj):
+    name = get_layer_name(layer_obj)
+    # kind = get_layer_kind(layer_obj)
+
+    label = f"{name}"
+
+    if is_missing_layer(layer_obj):
+        return "**MISSING**" + label
+    elif is_temp_layer(layer_obj):
+        return "* " + label
+    else:
+        return label
+
+
+def is_missing_layer(layer_obj):
+    cache_filepath = Path(bpy.path.abspath(
+        layer_obj.data.filepath)).resolve()
+    return not cache_filepath.is_file()
+
+
+def is_temp_layer(layer_obj):
+    cache_filepath = Path(bpy.path.abspath(
+        layer_obj.data.filepath)).resolve()
+    cache_dirpath = Path(get_cache_dir())
+    return cache_dirpath in cache_filepath.parents
+
+
+def set_layer_prop_value(layer_obj: bpy.types.Object, prop: str, value):
+    node_group = layer_obj.modifiers[0].node_group
+    layer_node = get_nodes_by_type(node_group, "BioxelNodes__Layer")[0]
+    layer_node.inputs[prop].default_value = value
+
+
+def get_layer_obj(current_obj: bpy.types.Object):
+    if current_obj:
+        if current_obj.get('bioxel_layer') and current_obj.parent:
+            if current_obj.parent.get('bioxel_container'):
+                return current_obj
+    return None
+
+
+def get_container_layer_objs(container_obj: bpy.types.Object):
+    layer_objs = []
+    for obj in bpy.data.objects:
+        if obj.parent == container_obj and get_layer_obj(obj):
+            layer_objs.append(obj)
+
+    return layer_objs
+
+
+def get_all_layer_objs():
+    layer_objs = []
+    for obj in bpy.data.objects:
+        if get_layer_obj(obj):
+            layer_objs.append(obj)
+
+    return layer_objs
+
+
+def add_driver(target, target_prop, var_sources, expression):
+    driver = target.driver_add(target_prop)
+    is_vector = isinstance(driver, list)
+    drivers = driver if is_vector else [driver]
+
+    for i, driver in enumerate(drivers):
+        for j, var_source in enumerate(var_sources):
+
+            source = var_source['source']
+            prop = var_source['prop']
+
+            var = driver.driver.variables.new()
+            var.name = f"var{j}"
+
+            var.targets[0].id_type = source.id_type
+            var.targets[0].id = source
+            var.targets[0].data_path = f'["{prop}"][{i}]'\
+                if is_vector else f'["{prop}"]'
+
+        driver.driver.expression = expression
+
+
+def add_direct_driver(target, target_prop, source, source_prop):
+    drivers = [
+        {
+            "source": source,
+            "prop": source_prop
+        }
+    ]
+    expression = "var0"
+    add_driver(target, target_prop, drivers, expression)
+
+
+def read_file_prop(content: str):
+    props = {}
+    for line in content.split("\n"):
+        line = line.replace(" ", "")
+        p = line.split("=")[0]
+        if p != "":
+            v = line.split("=")[-1]
+            props[p] = v
+    return props
+
+
+def write_file_prop(props: dict):
+    lines = []
+    for p, v in props.items():
+        lines.append(f"{p} = {v}")
+    return "\n".join(lines)
+
+
+def set_file_prop(prop, value):
+    if bpy.data.texts.get("BioxelNodes") is None:
+        bpy.data.texts.new("BioxelNodes")
+
+    props = read_file_prop(bpy.data.texts["BioxelNodes"].as_string())
+    props[prop] = value
+    bpy.data.texts["BioxelNodes"].clear()
+    bpy.data.texts["BioxelNodes"].write(write_file_prop(props))
+
+
+def get_file_prop(prop):
+    if bpy.data.texts.get("BioxelNodes") is None:
+        bpy.data.texts.new("BioxelNodes")
+
+    props = read_file_prop(bpy.data.texts["BioxelNodes"].as_string())
+    return props.get(prop)
+
+
+def 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

@@ -5,10 +5,13 @@ from bpy_extras.io_utils import axis_conversion
 from mathutils import Matrix, Vector
 
 
-from .layer import Layer, get_container_layer_objs, layer_to_obj, obj_to_layer
-from ..nodes import custom_nodes
-from .node import get_nodes_by_type, move_node_to_node
-
+from .layer import Layer, layer_to_obj, obj_to_layer
+from .common 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",
@@ -66,51 +69,6 @@ def calc_bbox_verts(origin: tuple, size: tuple):
     return bbox_verts
 
 
-def get_container_objs_from_selection():
-    container_objs = []
-    for obj in bpy.context.selected_objects:
-        if get_container_obj(obj):
-            container_objs.append(obj)
-
-    return list(set(container_objs))
-
-
-def get_container_obj(current_obj):
-    if current_obj:
-        if current_obj.get('bioxel_container'):
-            return current_obj
-        elif current_obj.get('bioxel_layer'):
-            parent = current_obj.parent
-            return parent if parent.get('bioxel_container') else None
-    return None
-
-
-def add_layers(layers: list[Layer],
-               container_obj: bpy.types.Object,
-               cache_dir: str):
-
-    container_node_group = container_obj.modifiers[0].node_group
-
-    for i, layer in enumerate(layers):
-        layer_obj = layer_to_obj(layer, container_obj, cache_dir)
-        mask_node = custom_nodes.add_node(container_node_group,
-                                          NODE_TYPE[layer.kind])
-        mask_node.label = layer_obj.name
-        mask_node.inputs[0].default_value = layer_obj
-
-        # Connect to output if no output linked
-        output_node = get_nodes_by_type(container_node_group,
-                                        'NodeGroupOutput')[0]
-        if len(output_node.inputs[0].links) == 0:
-            container_node_group.links.new(mask_node.outputs[0],
-                                           output_node.inputs[0])
-            move_node_to_node(mask_node, output_node, (-300, 0))
-        else:
-            move_node_to_node(mask_node, output_node, (0, -100 * (i+1)))
-
-    return container_obj
-
-
 def obj_to_container(container_obj: bpy.types.Object):
     layer_objs = get_container_layer_objs(container_obj)
     layers = [obj_to_layer(obj) for obj in layer_objs]
@@ -119,8 +77,38 @@ def obj_to_container(container_obj: bpy.types.Object):
     return container
 
 
+def add_layers(layers: list[Layer],
+               container_obj: bpy.types.Object,
+               cache_dir: str):
+
+    node_group = container_obj.modifiers[0].node_group
+    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 = add_node_to_graph("FetchLayer",
+                                       node_group,
+                                       get_use_link())
+        fetch_node.label = get_layer_prop_value(layer_obj, "name")
+        fetch_node.inputs[0].default_value = layer_obj
+
+        if len(output_node.inputs[0].links) == 0:
+            node_group.links.new(fetch_node.outputs[0],
+                                 output_node.inputs[0])
+            move_node_to_node(fetch_node, output_node, (-600, 0))
+        else:
+            move_node_to_node(fetch_node, output_node, (0, -100 * (i+1)))
+
+    return container_obj
+
+
 def container_to_obj(container: Container,
                      scene_scale: float,
+                     step_size: float,
                      cache_dir: str):
     # Wrapper a Container
 
@@ -151,30 +139,33 @@ def container_to_obj(container: Container,
     container_obj.name = container.name
     container_obj.data.name = container.name
     container_obj.show_in_front = True
+
+    container_obj.lock_location[0] = True
+    container_obj.lock_location[1] = True
+    container_obj.lock_location[2] = True
+
+    container_obj.lock_rotation[0] = True
+    container_obj.lock_rotation[1] = True
+    container_obj.lock_rotation[2] = True
+
+    container_obj.lock_scale[0] = True
+    container_obj.lock_scale[1] = True
+    container_obj.lock_scale[2] = True
+
     container_obj['bioxel_container'] = True
+    container_obj["scene_scale"] = scene_scale
+    container_obj["step_size"] = step_size
 
-    bpy.ops.node.new_geometry_nodes_modifier()
-    container_node_group = container_obj.modifiers[0].node_group
-    input_node = get_nodes_by_type(container_node_group,
-                                   'NodeGroupInput')[0]
-    container_node_group.links.remove(
-        input_node.outputs[0].links[0])
+    modifier = container_obj.modifiers.new("GeometryNodes", 'NODES')
+    node_group = bpy.data.node_groups.new('GeometryNodes', 'GeometryNodeTree')
+    node_group.interface.new_socket(name="Output",
+                                    in_out="OUTPUT",
+                                    socket_type="NodeSocketGeometry")
+    modifier.node_group = node_group
+    node_group.nodes.new("NodeGroupOutput")
 
-    for i, layer in enumerate(container.layers):
-        layer_obj = layer_to_obj(layer, container_obj, cache_dir)
-        mask_node = custom_nodes.add_node(container_node_group,
-                                          NODE_TYPE[layer.kind])
-        mask_node.label = layer_obj.name
-        mask_node.inputs[0].default_value = layer_obj
-
-        # Connect to output if no output linked
-        output_node = get_nodes_by_type(container_node_group,
-                                        'NodeGroupOutput')[0]
-        if len(output_node.inputs[0].links) == 0:
-            container_node_group.links.new(mask_node.outputs[0],
-                                           output_node.inputs[0])
-            move_node_to_node(mask_node, output_node, (-300, 0))
-        else:
-            move_node_to_node(mask_node, output_node, (0, -100 * (i+1)))
+    container_obj = add_layers(container.layers,
+                               container_obj=container_obj,
+                               cache_dir=cache_dir)
 
     return container_obj

bioxelnodes/bioxelutils/layer.py

@@ -7,35 +7,11 @@ import pyopenvdb as vdb
 from pathlib import Path
 from uuid import uuid4
 
-from ..nodes import custom_nodes
 from ..bioxel.layer import Layer
-from .node import get_nodes_by_type, move_node_between_nodes
-
-
-def get_layer_obj(current_obj: bpy.types.Object):
-    if current_obj:
-        if current_obj.get('bioxel_layer') and current_obj.parent:
-            if current_obj.parent.get('bioxel_container'):
-                return current_obj
-    return None
-
-
-def get_container_layer_objs(container_obj: bpy.types.Object):
-    layer_objs = []
-    for obj in bpy.context.scene.objects:
-        if obj.parent == container_obj and get_layer_obj(obj):
-            layer_objs.append(obj)
-
-    return layer_objs
-
-
-def get_all_layer_objs():
-    layer_objs = []
-    for obj in bpy.context.scene.objects:
-        if get_layer_obj(obj):
-            layer_objs.append(obj)
-
-    return layer_objs
+from ..utils import get_use_link
+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):
@@ -51,7 +27,11 @@ def obj_to_layer(layer_obj: bpy.types.Object):
             grids, base_metadata = vdb.readAll(str(f))
             grid = grids[0]
             metadata = grid.metadata
-            data_frame = np.ndarray(grid["data_shape"], np.float32)
+            if grid["layer_kind"] in ['label', 'scalar']:
+                data_shape = grid["data_shape"]
+            else:
+                data_shape = tuple(list(grid["data_shape"]) + [3])
+            data_frame = np.ndarray(data_shape, np.float32)
             grid.copyToArray(data_frame)
             data_frames += (data_frame,)
         data = np.stack(data_frames)
@@ -59,15 +39,24 @@ def obj_to_layer(layer_obj: bpy.types.Object):
         grids, base_metadata = vdb.readAll(str(cache_filepath))
         grid = grids[0]
         metadata = grid.metadata
-        data = np.ndarray(grid["data_shape"], np.float32)
+        if grid["layer_kind"] in ['label', 'scalar']:
+            data_shape = grid["data_shape"]
+        else:
+            data_shape = tuple(list(grid["data_shape"]) + [3])
+        data = np.ndarray(data_shape, np.float32)
         grid.copyToArray(data)
         data = np.expand_dims(data, axis=0)  # expend frame
 
-    name = metadata["layer_name"]
-    kind = metadata["layer_kind"]
+    name = get_layer_prop_value(layer_obj, "name") \
+        or metadata["layer_name"]
+    kind = get_layer_prop_value(layer_obj, "kind") \
+        or metadata["layer_kind"]
     affine = metadata["layer_affine"]
-    dtype = metadata.get("data_dtype") or "float32"
-    offset = metadata.get("data_offset") or 0
+    dtype = get_layer_prop_value(layer_obj, "dtype") \
+        or metadata.get("data_dtype") or "float32"
+    offset = get_layer_prop_value(layer_obj, "offset") \
+        or metadata.get("data_offset") or 0
+
     data = data - np.full_like(data, offset)
     data = data.astype(dtype)
 
@@ -110,6 +99,7 @@ def layer_to_obj(layer: Layer,
         "data_offset": offset
     }
 
+    layer_display_name = f"{container_obj.name}_{layer.name}"
     if layer.frame_count > 1:
         print(f"Saving the Cache of {layer.name}...")
         vdb_name = str(uuid4())
@@ -118,8 +108,14 @@ def layer_to_obj(layer: Layer,
 
         cache_filepaths = []
         for f in range(layer.frame_count):
-            grid = vdb.FloatGrid()
-            grid.copyFromArray(data[f, :, :, :].copy().astype(np.float32))
+            if layer.kind in ['label', 'scalar']:
+                grid = vdb.FloatGrid()
+                grid.copyFromArray(data[f, :, :, :].copy().astype(np.float32))
+            else:
+                # color
+                grid = vdb.Vec3SGrid()
+                grid.copyFromArray(
+                    data[f, :, :, :, :].copy().astype(np.float32))
             grid.transform = vdb.createLinearTransform(
                 layer.affine.transpose())
             grid.metadata = metadata
@@ -130,17 +126,14 @@ def layer_to_obj(layer: Layer,
             vdb.write(str(cache_filepath), grids=[grid])
             cache_filepaths.append(cache_filepath)
 
-        print(f"Loading the Cache of {layer.name}...")
-        files = [{"name": str(cache_filepath.name), "name": str(cache_filepath.name)}
-                 for cache_filepath in cache_filepaths]
-
-        bpy.ops.object.volume_import(filepath=str(cache_filepaths[0]),
-                                     directory=str(cache_filepaths[0].parent),
-                                     files=files, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-
     else:
-        grid = vdb.FloatGrid()
-        grid.copyFromArray(data[0, :, :, :].copy().astype(np.float32))
+        if layer.kind in ['label', 'scalar']:
+            grid = vdb.FloatGrid()
+            grid.copyFromArray(data[0, :, :, :].copy().astype(np.float32))
+        else:
+            # color
+            grid = vdb.Vec3SGrid()
+            grid.copyFromArray(data[0, :, :, :, :].copy().astype(np.float32))
         grid.transform = vdb.createLinearTransform(
             layer.affine.transpose())
         grid.metadata = metadata
@@ -151,52 +144,35 @@ def layer_to_obj(layer: Layer,
         vdb.write(str(cache_filepath), grids=[grid])
         cache_filepaths = [cache_filepath]
 
-        print(f"Loading the Cache of {layer.name}...")
-        bpy.ops.object.volume_import(filepath=str(cache_filepaths[0]),
-                                     align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
+    layer_data = bpy.data.volumes.new(layer_display_name)
+    layer_data.render.space = 'WORLD'
+    scene_scale = container_obj.get("scene_scale") or 0.01
+    step_size = container_obj.get("step_size") or 1
+    layer_data.render.step_size = scene_scale * step_size
+    layer_data.sequence_mode = 'REPEAT'
+    layer_data.filepath = str(cache_filepaths[0])
 
-    layer_obj = bpy.context.active_object
-    layer_obj.data.sequence_mode = 'REPEAT'
-
-    # Set props to VDB object
-    layer_obj.name = f"{container_obj.name}_{layer.name}"
-    layer_obj.data.name = f"{container_obj.name}_{layer.name}"
-
-    layer_obj.lock_location[0] = True
-    layer_obj.lock_location[1] = True
-    layer_obj.lock_location[2] = True
-    layer_obj.lock_rotation[0] = True
-    layer_obj.lock_rotation[1] = True
-    layer_obj.lock_rotation[2] = True
-    layer_obj.lock_scale[0] = True
-    layer_obj.lock_scale[1] = True
-    layer_obj.lock_scale[2] = True
-
-    layer_obj.visible_camera = False
-    layer_obj.visible_diffuse = False
-    layer_obj.visible_glossy = False
-    layer_obj.visible_transmission = False
-    layer_obj.visible_volume_scatter = False
-    layer_obj.visible_shadow = False
-
-    layer_obj.hide_select = True
-    layer_obj.hide_render = True
-    layer_obj.hide_viewport = True
+    if layer.frame_count > 1:
+        layer_data.is_sequence = True
+        layer_data.frame_duration = layer.frame_count
+    else:
+        layer_data.is_sequence = False
 
+    layer_obj = bpy.data.objects.new(layer_display_name, layer_data)
     layer_obj['bioxel_layer'] = True
-    layer_obj.parent = container_obj
-
-    for collection in layer_obj.users_collection:
-        collection.objects.unlink(layer_obj)
-
-    for collection in container_obj.users_collection:
-        collection.objects.link(layer_obj)
 
     print(f"Creating Node for {layer.name}...")
-    bpy.ops.node.new_geometry_nodes_modifier()
-    node_group = layer_obj.modifiers[0].node_group
-    layer_node = custom_nodes.add_node(node_group,
-                                          "BioxelNodes__Layer")
+    modifier = layer_obj.modifiers.new("GeometryNodes", 'NODES')
+    node_group = bpy.data.node_groups.new('GeometryNodes', 'GeometryNodeTree')
+    node_group.interface.new_socket(name="Cache",
+                                    in_out="INPUT",
+                                    socket_type="NodeSocketGeometry")
+    node_group.interface.new_socket(name="Layer",
+                                    in_out="OUTPUT",
+                                    socket_type="NodeSocketGeometry")
+    modifier.node_group = node_group
+
+    layer_node = add_node_to_graph("_Layer", node_group, get_use_link())
 
     layer_node.inputs['name'].default_value = layer.name
     layer_node.inputs['shape'].default_value = layer.shape
@@ -207,19 +183,18 @@ def layer_to_obj(layer: Layer,
             affine_key = f"affine{i}{j}"
             layer_node.inputs[affine_key].default_value = layer.affine[j, i]
 
-    layer_node.inputs['id'].default_value = random.randint(-200000000,
-                                                              200000000)
+    layer_node.inputs['unique'].default_value = random.uniform(0, 1)
     layer_node.inputs['bioxel_size'].default_value = layer.bioxel_size[0]
     layer_node.inputs['dtype'].default_value = layer.dtype.str
     layer_node.inputs['dtype_num'].default_value = layer.dtype.num
+    layer_node.inputs['frame_count'].default_value = layer.frame_count
+    layer_node.inputs['channel_count'].default_value = layer.channel_count
     layer_node.inputs['offset'].default_value = max(0, -layer.min)
     layer_node.inputs['min'].default_value = layer.min
     layer_node.inputs['max'].default_value = layer.max
 
-    input_node = get_nodes_by_type(node_group,
-                                   'NodeGroupInput')[0]
-    output_node = get_nodes_by_type(node_group,
-                                    'NodeGroupOutput')[0]
+    input_node = node_group.nodes.new("NodeGroupInput")
+    output_node = node_group.nodes.new("NodeGroupOutput")
 
     node_group.links.new(input_node.outputs[0],
                          layer_node.inputs[0])
@@ -229,4 +204,6 @@ def layer_to_obj(layer: Layer,
     move_node_between_nodes(
         layer_node, [input_node, output_node])
 
+    layer_obj.parent = container_obj
+
     return layer_obj

bioxelnodes/bioxelutils/node.py

@@ -1,26 +1,68 @@
-def move_node_to_node(node, target_node, offset=(0, 0)):
-    node.location.x = target_node.location.x + offset[0]
-    node.location.y = target_node.location.y + offset[1]
+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 move_node_between_nodes(node, target_nodes, offset=(0, 0)):
-    xs = []
-    ys = []
-    for target_node in target_nodes:
-        xs.append(target_node.location.x)
-        ys.append(target_node.location.y)
+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
 
-    node.location.x = sum(xs) / len(xs) + offset[0]
-    node.location.y = sum(ys) / len(ys) + offset[1]
+    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 get_node_type(node):
-    node_type = type(node).__name__
-    if node_type == "GeometryNodeGroup":
-        node_type = node.node_tree.name
-
-    return node_type
+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 get_nodes_by_type(node_group, type_name: str):
-    return [node for node in node_group.nodes if get_node_type(node) == type_name]
+def 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 = "0.3.3"
+version = "1.0.0"
 name = "Bioxel Nodes"
 tagline = "For scientific volumetric data visualization in Blender"
 maintainer = "Ma Nan <icrdr2010@outlook.com>"
@@ -30,9 +30,8 @@ wheels = [
   "./wheels/tifffile-2024.7.24-py3-none-any.whl",
   "./wheels/pyometiff-1.0.0-py3-none-any.whl",
   "./wheels/mrcfile-1.5.1-py2.py3-none-any.whl",
-  "./wheels/transforms3d-0.4.2-py3-none-any.whl",
+  "./wheels/transforms3d-0.4.2-py3-none-any.whl"
 ]
 
 [permissions]
 files = "Import/export volume data from/to disk"
-

bioxelnodes/constants.py

@@ -0,0 +1,224 @@
+from pathlib import Path
+
+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 = [
+    {
+        'label': 'Component',
+        'icon': 'OUTLINER_DATA_VOLUME',
+        'items': [
+            {
+                'label': 'Cutout by Threshold',
+                'icon': 'EMPTY_SINGLE_ARROW',
+                'name': 'CutoutByThreshold',
+                'description': ''
+            },
+            {
+                'label': 'Cutout by Range',
+                'icon': 'IPO_CONSTANT',
+                'name': 'CutoutByRange',
+                'description': ''
+            },
+            {
+                'label': 'Cutout by Color',
+                'icon': 'COLOR',
+                'name': 'CutoutByColor',
+                'description': ''
+            },
+            "separator",
+            {
+                'label': 'To Surface',
+                'icon': 'MESH_DATA',
+                'name': 'ToSurface',
+                'description': ''
+            },
+            {
+                'label': 'Join Component',
+                'icon': 'CONSTRAINT_BONE',
+                'name': 'JoinComponent',
+                'description': ''
+            },
+            {
+                'label': 'Slice',
+                'icon': 'TEXTURE',
+                'name': 'Slice',
+                'description': ''
+            }
+        ]
+    },
+    {
+        'label': 'Properties',
+        'icon': 'PROPERTIES',
+        'items': [
+            {
+                'label': 'Set Properties',
+                'icon': 'PROPERTIES',
+                'name': 'SetProperties',
+                'description': ''
+            },
+            "separator",
+            {
+                'label': 'Set Color',
+                'icon': 'IPO_SINE',
+                'name': 'SetColor',
+                'description': ''
+            },
+            {
+                'label': 'Set Color by Color',
+                'icon': 'IPO_QUINT',
+                'name': 'SetColorByColor',
+                'description': ''
+            },
+            {
+                'label': 'Set Color by Ramp 2',
+                'icon': 'IPO_QUAD',
+                'name': 'SetColorByRamp2',
+                'description': ''
+            },
+            {
+                'label': 'Set Color by Ramp 3',
+                'icon': 'IPO_CUBIC',
+                'name': 'SetColorByRamp3',
+                'description': ''
+            },
+            {
+                'label': 'Set Color by Ramp 4',
+                'icon': 'IPO_QUART',
+                'name': 'SetColorByRamp4',
+                'description': ''
+            },
+            {
+                'label': 'Set Color by Ramp 5',
+                'icon': 'IPO_QUINT',
+                'name': 'SetColorByRamp5',
+                'description': ''
+            }
+        ]
+    },
+    {
+        'label': 'Surface',
+        'icon': 'MESH_DATA',
+        'items': [
+            {
+                'label': 'Membrane Shader',
+                'icon': 'NODE_MATERIAL',
+                'name': 'AssignMembraneShader',
+                'description': ''
+            },
+            {
+                'label': 'Solid Shader',
+                'icon': 'SHADING_SOLID',
+                'name': 'AssignSolidShader',
+                'description': ''
+            },
+            {
+                'label': 'Slime Shader',
+                'icon': 'OUTLINER_DATA_META',
+                'name': 'AssignSlimeShader',
+                'description': ''
+            },
+
+        ]
+    },
+    {
+        'label': 'Transform',
+        'icon': 'EMPTY_AXIS',
+        'items': [
+            {
+                'label': 'Transform',
+                'icon': 'EMPTY_AXIS',
+                'name': 'Transform',
+                'description': ''
+            },
+            {
+                'label': 'Transform Parent',
+                'icon': 'ORIENTATION_PARENT',
+                'name': 'TransformParent',
+                'description': ''
+            },
+            {
+                'label': 'ReCenter',
+                'icon': 'PROP_CON',
+                'name': 'ReCenter',
+                'description': ''
+            }
+        ]
+    },
+    {
+        'label': 'Cutters',
+        'icon': 'MOD_BEVEL',
+        'items': [
+            {
+                'label': 'Cut',
+                'icon': 'MOD_BEVEL',
+                'name': 'Cut',
+                'description': ''
+            },
+            "separator",
+            {
+                'label': 'Primitive Cutter',
+                'icon': 'MOD_LINEART',
+                'name': 'PrimitiveCutter',
+                'description': ''
+            },
+            {
+                'label': 'Object Cutter',
+                'icon': 'MESH_PLANE',
+                'name': 'ObjectCutter',
+                'description': ''
+            }
+        ]
+    },
+    {
+        'label': 'Utils',
+        'icon': 'MODIFIER',
+        'items': [
+            {
+                'label': 'Pick Surface',
+                'icon': 'OUTLINER_OB_MESH',
+                'name': 'PickSurface',
+                'description': ''
+            },
+            {
+                'label': 'Pick Volume',
+                'icon': 'OUTLINER_OB_VOLUME',
+                'name': 'PickVolume',
+                'description': ''
+            },
+            {
+                'label': 'Pick Shape Wire',
+                'icon': 'FILE_VOLUME',
+                'name': 'PickShapeWire',
+                'description': ''
+            },
+            {
+                'label': 'Pick Bbox Wire',
+                'icon': 'MESH_CUBE',
+                'name': 'PickBboxWire',
+                'description': ''
+            },
+            "separator",
+            {
+                'label': 'Inflate',
+                'icon': 'OUTLINER_OB_META',
+                'name': 'Inflate',
+                'description': ''
+            },
+            {
+                'label': 'Smooth',
+                'icon': 'MOD_SMOOTH',
+                'name': 'Smooth',
+                'description': ''
+            },
+            {
+                'label': 'Remove Small Island',
+                'icon': 'FORCE_LENNARDJONES',
+                'name': 'RemoveSmallIsland',
+                'description': ''
+            }
+        ]
+    }
+]

bioxelnodes/customnodes/__init__.py

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

bioxelnodes/customnodes/menus.py

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

bioxelnodes/customnodes/nodes.py

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

bioxelnodes/exceptions.py

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

bioxelnodes/menus.py

@@ -1,156 +1,160 @@
 import bpy
 
-from .bioxelutils.container import get_container_objs_from_selection
-from .operators.layer import (CombineLabels, SignScalar,
+from .constants import MENU_ITEMS, NODE_LIB_FILENAME
+from .node_menu import NodeMenu
+
+from .bioxelutils.common import (get_container_obj,
+                                 get_container_layer_objs, get_layer_label,
+                                 get_layer_prop_value)
+from .operators.layer import (FetchLayer, RelocateLayer, RetimeLayer, RenameLayer,
+                              RemoveSelectedLayers, SaveSelectedLayersCache,
+                              ResampleLayer, SignScalar, CombineLabels,
                               FillByLabel, FillByThreshold, FillByRange)
-from .operators.container import (SaveContainer, LoadContainer,
+from .operators.container import (AddLocator, AddSlicer, ExtractShapeWire,
+                                  SaveContainerLayersCache, RemoveContainerMissingLayers,
+                                  SaveContainer, LoadContainer,
                                   AddPieCutter, AddPlaneCutter,
                                   AddCylinderCutter, AddCubeCutter, AddSphereCutter,
-                                  PickBboxWire, PickMesh, PickVolume)
-from .operators.io import (ExportVolumetricData,
-                           ImportAsLabelLayer, ImportAsScalarLayer)
-from .operators.misc import (CleanAllCaches,
-                             ReLinkNodes, SaveCaches, SaveStagedData)
+                                  ExtractBboxWire, ExtractSurface, ExtractVolume, ContainerProps)
+
+from .operators.io import (ImportAsLabel, ImportAsScalar, ImportAsColor)
+from .operators.misc import (CleanTemp,
+                             ReLinkNodeLib, RemoveAllMissingLayers, RenderSettingPreset, SaveAllLayersCache, SaveNodeLib, SliceViewer)
 
 
-def container_is_selected():
-    container_objs = get_container_objs_from_selection()
-    return len(container_objs) > 0
+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 PickFromContainerMenu(bpy.types.Menu):
+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(PickVolume.bl_idname)
-        layout.operator(PickBboxWire.bl_idname)
-
-
-class ModifyLayerMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_MODIFY_LAYERS"
-    bl_label = "Modify Layer"
-
-    def draw(self, context):
-        layout = self.layout
-        layout.operator(SignScalar.bl_idname)
-        layout.operator(FillByThreshold.bl_idname)
-        layout.operator(FillByRange.bl_idname)
-        layout.operator(FillByLabel.bl_idname)
-        layout.operator(CombineLabels.bl_idname)
+        layout.operator(ExtractSurface.bl_idname)
+        layout.operator(ExtractVolume.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 Cutter to Container"
+    bl_label = "Add a Cutter"
 
     def draw(self, context):
         layout = self.layout
-        layout.operator(AddPlaneCutter.bl_idname, text="Plane Cutter")
-        layout.operator(AddCylinderCutter.bl_idname, text="Cylinder Cutter")
-        layout.operator(AddCubeCutter.bl_idname, text="Cube Cutter")
-        layout.operator(AddSphereCutter.bl_idname, text="Sphere Cutter")
-        layout.operator(AddPieCutter.bl_idname, text="Pie Cutter")
+        layout.operator(AddPlaneCutter.bl_idname,
+                        icon=AddPlaneCutter.bl_icon, text="Plane Cutter")
+        layout.operator(AddCylinderCutter.bl_idname,
+                        icon=AddCylinderCutter.bl_icon, text="Cylinder Cutter")
+        layout.operator(AddCubeCutter.bl_idname,
+                        icon=AddCubeCutter.bl_icon, text="Cube Cutter")
+        layout.operator(AddSphereCutter.bl_idname,
+                        icon=AddSphereCutter.bl_icon, text="Sphere Cutter")
+        layout.operator(AddPieCutter.bl_idname,
+                        icon=AddPieCutter.bl_icon, text="Pie Cutter")
 
 
 class ImportLayerMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_LAYERS"
-    bl_label = "Import Volumetric Data"
+    bl_idname = "BIOXELNODES_MT_IMPORTLAYER"
+    bl_label = "Import Volumetric Data (Init)"
+    bl_icon = "FILE_NEW"
 
     def draw(self, context):
         layout = self.layout
-        layout.operator(ImportAsScalarLayer.bl_idname, text="as Scalar")
-        layout.operator(ImportAsLabelLayer.bl_idname, text="as Label")
+        layout.operator(ImportAsScalar.bl_idname,
+                        text="as Scalar")
+        layout.operator(ImportAsLabel.bl_idname,
+                        text="as Label")
+        layout.operator(ImportAsColor.bl_idname,
+                        text="as Color")
 
 
-class BioxelNodesView3DMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_VIEW3D"
-    bl_label = "Bioxel Nodes"
+class AddLayerMenu(bpy.types.Menu):
+    bl_idname = "BIOXELNODES_MT_ADDLAYER"
+    bl_label = "Import Volumetric Data (Add)"
+    bl_icon = "FILE_NEW"
 
     def draw(self, context):
         layout = self.layout
-        is_selected = container_is_selected()
-        layout.operator(ImportAsScalarLayer.bl_idname,
-                        text=ImportAsScalarLayer.bl_label+" (Add to)"
-                        if is_selected else ImportAsScalarLayer.bl_label+" (Init)")
-        layout.operator(ImportAsLabelLayer.bl_idname,
-                        text=ImportAsLabelLayer.bl_label+" (Add to)"
-                        if is_selected else ImportAsLabelLayer.bl_label+" (Init)")
-        layout.separator()
-        layout.operator(AddPlaneCutter.bl_idname)
-        layout.operator(AddCylinderCutter.bl_idname)
-        layout.operator(AddCubeCutter.bl_idname)
-        layout.operator(AddSphereCutter.bl_idname)
-        layout.operator(AddPieCutter.bl_idname)
-        layout.separator()
-        layout.operator(PickMesh.bl_idname)
-        layout.operator(PickVolume.bl_idname)
-        layout.operator(PickBboxWire.bl_idname)
-        layout.separator()
-        layout.operator(SaveCaches.bl_idname)
+        layout.operator(ImportAsScalar.bl_idname,
+                        text="as Scalar")
+        layout.operator(ImportAsLabel.bl_idname,
+                        text="as Label")
+        layout.operator(ImportAsColor.bl_idname,
+                        text="as Color")
 
 
-class BioxelNodesOutlinerMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_OUTLINER"
-    bl_label = "Bioxel Nodes"
+class ModifyLayerMenu(bpy.types.Menu):
+    bl_idname = "BIOXELNODES_MT_MODIFYLAYER"
+    bl_label = "Modify Layer"
+    bl_icon = "FILE_NEW"
 
     def draw(self, context):
         layout = self.layout
-        is_selected = container_is_selected()
-        layout.operator(ImportAsScalarLayer.bl_idname,
-                        text=ImportAsScalarLayer.bl_label+" (Add to)"
-                        if is_selected else ImportAsScalarLayer.bl_label+" (Init)")
-        layout.operator(ImportAsLabelLayer.bl_idname,
-                        text=ImportAsLabelLayer.bl_label+" (Add to)"
-                        if is_selected else ImportAsLabelLayer.bl_label+" (Init)")
+        layout.operator(SignScalar.bl_idname,
+                        icon=SignScalar.bl_icon)
+        layout.operator(FillByThreshold.bl_idname,
+                        icon=FillByThreshold.bl_icon)
+        layout.operator(FillByRange.bl_idname,
+                        icon=FillByRange.bl_icon)
+        layout.operator(FillByLabel.bl_idname,
+                        icon=FillByLabel.bl_icon)
+        layout.operator(CombineLabels.bl_idname,
+                        icon=CombineLabels.bl_icon)
+
+
+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()
-        layout.operator(AddPlaneCutter.bl_idname)
-        layout.operator(AddCylinderCutter.bl_idname)
-        layout.operator(AddCubeCutter.bl_idname)
-        layout.operator(AddSphereCutter.bl_idname)
-        layout.operator(AddPieCutter.bl_idname)
-        layout.separator()
-        layout.operator(PickMesh.bl_idname)
-        layout.operator(PickVolume.bl_idname)
-        layout.operator(PickBboxWire.bl_idname)
-        layout.separator()
-        layout.operator(SaveCaches.bl_idname)
-        layout.separator()
-        layout.operator(SignScalar.bl_idname)
-        layout.operator(FillByThreshold.bl_idname)
-        layout.operator(FillByRange.bl_idname)
-        layout.operator(FillByLabel.bl_idname)
-        layout.operator(CombineLabels.bl_idname)
+        for version in versions:
+            op = layout.operator(ReLinkNodeLib.bl_idname,
+                                 text=version["label"])
+            op.node_lib_filename = version["filename"]
 
 
-def TOPBAR_FILE_IMPORT(self, context):
-    layout = self.layout
-    is_selected = container_is_selected()
+class RenderSettingMenu(bpy.types.Menu):
+    bl_idname = "BIOXELNODES_MT_RENDER"
+    bl_label = "Render Setting Presets"
 
-    layout.separator()
-    layout.menu(ImportLayerMenu.bl_idname, text="Volumetric Data as Bioxel (Add to)"
-                if is_selected else "Volumetric Data as Bioxel (Init)")
+    def draw(self, context):
+        layout = self.layout
+        for k, v in RenderSettingPreset.PRESETS.items():
+            op = layout.operator(RenderSettingPreset.bl_idname,
+                                 text=v)
+            op.preset = k
 
 
-def TOPBAR_FILE_EXPORT(self, context):
-    layout = self.layout
-    layout.separator()
-    layout.operator(ExportVolumetricData.bl_idname,
-                    text="Bioxel Layer (.vdb)")
+class DangerZoneMenu(bpy.types.Menu):
+    bl_idname = "BIOXELNODES_MT_DANGER"
+    bl_label = "Danger Zone"
 
-
-def VIEW3D_OBJECT(self, context):
-    layout = self.layout
-    layout.separator()
-    layout.menu(BioxelNodesView3DMenu.bl_idname, icon="FILE_VOLUME")
-
-
-def OUTLINER_OBJECT(self, context):
-    layout = self.layout
-    layout.separator()
-    layout.menu(BioxelNodesOutlinerMenu.bl_idname, icon="FILE_VOLUME")
+    def draw(self, context):
+        layout = self.layout
+        layout.operator(CleanTemp.bl_idname)
 
 
 class BioxelNodesTopbarMenu(bpy.types.Menu):
@@ -159,21 +163,24 @@ class BioxelNodesTopbarMenu(bpy.types.Menu):
 
     def draw(self, context):
         layout = self.layout
-        is_selected = container_is_selected()
 
-        layout.menu(ImportLayerMenu.bl_idname, text=ImportLayerMenu.bl_label+" (Add to)"
-                    if is_selected else ImportLayerMenu.bl_label+" (Init)")
-        layout.separator()
+        layout.menu(ImportLayerMenu.bl_idname,
+                    icon=ImportLayerMenu.bl_icon)
         layout.operator(LoadContainer.bl_idname)
-        layout.operator(SaveContainer.bl_idname)
+
         layout.separator()
-        layout.menu(AddCutterMenu.bl_idname)
-        layout.menu(PickFromContainerMenu.bl_idname)
+        layout.operator(SaveAllLayersCache.bl_idname)
+        layout.operator(RemoveAllMissingLayers.bl_idname)
+
         layout.separator()
-        layout.operator(SaveStagedData.bl_idname)
-        layout.operator(ReLinkNodes.bl_idname)
+        layout.operator(SaveNodeLib.bl_idname)
+        layout.menu(ReLinkNodeLibMenu.bl_idname)
+
         layout.separator()
-        layout.operator(CleanAllCaches.bl_idname)
+        layout.menu(DangerZoneMenu.bl_idname)
+
+        layout.separator()
+        layout.menu(RenderSettingMenu.bl_idname)
 
 
 def TOPBAR(self, context):
@@ -181,17 +188,194 @@ def TOPBAR(self, context):
     layout.menu(BioxelNodesTopbarMenu.bl_idname)
 
 
+class NodeHeadMenu(bpy.types.Menu):
+    bl_idname = "BIOXELNODES_MT_NODE_HEAD"
+    bl_label = "Bioxel Nodes"
+    bl_icon = "FILE_VOLUME"
+
+    def draw(self, context):
+
+        layout = self.layout
+        layout.menu(AddLayerMenu.bl_idname,
+                    icon=AddLayerMenu.bl_icon)
+        layout.operator(SaveContainer.bl_idname)
+
+        layout.separator()
+        layout.operator(ContainerProps.bl_idname)
+        layout.menu(ExtractFromContainerMenu.bl_idname)
+
+        layout.separator()
+        layout.operator(SaveContainerLayersCache.bl_idname,
+                        icon=SaveContainerLayersCache.bl_icon)
+        layout.operator(RemoveContainerMissingLayers.bl_idname)
+
+        layout.separator()
+        layout.operator(AddLocator.bl_idname,
+                        icon=AddLocator.bl_icon)
+        layout.operator(AddSlicer.bl_idname,
+                        icon=AddSlicer.bl_icon)
+        layout.menu(AddCutterMenu.bl_idname)
+
+        layout.separator()
+        layout.menu(FetchLayerMenu.bl_idname)
+
+
+class NodeContextMenu(bpy.types.Menu):
+    bl_idname = "BIOXELNODES_MT_NODE_CONTEXT"
+    bl_label = "Bioxel Nodes"
+    bl_icon = "FILE_VOLUME"
+
+    def draw(self, context):
+        layout = self.layout
+        layout.operator(SaveSelectedLayersCache.bl_idname,
+                        icon=SaveSelectedLayersCache.bl_icon)
+        layout.operator(RemoveSelectedLayers.bl_idname)
+
+        layout.separator()
+        layout.operator(RenameLayer.bl_idname,
+                        icon=RenameLayer.bl_icon)
+        layout.operator(RetimeLayer.bl_idname)
+        layout.operator(RelocateLayer.bl_idname)
+
+        layout.separator()
+        layout.operator(ResampleLayer.bl_idname,
+                        icon=ResampleLayer.bl_icon)
+        layout.operator(SignScalar.bl_idname)
+        layout.operator(FillByThreshold.bl_idname)
+        layout.operator(FillByRange.bl_idname)
+        layout.operator(FillByLabel.bl_idname)
+        layout.operator(CombineLabels.bl_idname)
+
+
+def NODE_CONTEXT(self, context):
+    container_obj = context.object
+    is_geo_nodes = context.area.ui_type == "GeometryNodeTree"
+    is_container = get_container_obj(container_obj)
+
+    if not is_geo_nodes or not is_container:
+        return
+
+    layout = self.layout
+    layout.separator()
+    layout.menu(NodeContextMenu.bl_idname)
+
+
+def NODE_HEAD(self, context):
+    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)
+    self.bl_label = "Group"
+
+    if not is_geo_nodes or not is_container:
+        return
+
+    if container_obj.modifiers[0].node_group != context.space_data.edit_tree:
+        return
+
+    self.bl_label = "Bioxel Nodes"
+
+    layer_list_UL = bpy.context.window_manager.bioxelnodes_layer_list_UL
+    layer_list = layer_list_UL.layer_list
+    layer_list.clear()
+
+    for layer_obj in get_container_layer_objs(container_obj):
+        layer_item = layer_list.add()
+        layer_item.label = get_layer_label(layer_obj)
+        layer_item.obj_name = layer_obj.name
+        layer_item.info_text = "\n".join([f"{prop}: {get_layer_prop_value(layer_obj, prop)}"
+                                          for prop in ["kind",
+                                                       "bioxel_size",
+                                                       "shape",
+                                                       "frame_count",
+                                                       "channel_count",
+                                                       "min", "max"]])
+
+    layout = self.layout
+    layout.label(text="Layer List")
+    split = layout.row()
+    split.template_list(listtype_name="BIOXELNODES_UL_layer_list",
+                        list_id="layer_list",
+                        dataptr=layer_list_UL,
+                        propname="layer_list",
+                        active_dataptr=layer_list_UL,
+                        active_propname="layer_list_active",
+                        item_dyntip_propname="info_text",
+                        rows=20)
+
+    # sidebar = split.column(align=True)
+    # sidebar.menu(AddLayerMenu.bl_idname,
+    #              icon=AddLayerMenu.bl_icon, text="")
+
+    # sidebar.operator(SaveContainerLayersCache.bl_idname,
+    #                  icon=SaveContainerLayersCache.bl_icon, text="")
+    # sidebar.operator(RemoveContainerMissingLayers.bl_idname,
+    #                  icon=RemoveContainerMissingLayers.bl_icon, text="")
+
+    # sidebar.separator()
+    # sidebar.operator(SaveSelectedLayersCache.bl_idname,
+    #                  icon=SaveSelectedLayersCache.bl_icon, text="")
+    # sidebar.operator(RemoveSelectedLayers.bl_idname,
+    #                  icon=RemoveSelectedLayers.bl_icon, text="")
+
+    # sidebar.separator()
+    # sidebar.operator(RenameLayer.bl_idname,
+    #                  icon=RenameLayer.bl_icon, text="")
+    # sidebar.operator(ResampleLayer.bl_idname,
+    #                  icon=ResampleLayer.bl_icon, text="")
+    # sidebar.operator(RetimeLayer.bl_idname,
+    #                  icon=RetimeLayer.bl_icon, text="")
+
+    # sidebar.separator()
+    # sidebar.operator(SignScalar.bl_idname,
+    #                  icon=SignScalar.bl_icon, text="")
+    # sidebar.operator(FillByThreshold.bl_idname,
+    #                  icon=FillByThreshold.bl_icon, text="")
+    # sidebar.operator(FillByRange.bl_idname,
+    #                  icon=FillByRange.bl_icon, text="")
+    # sidebar.operator(FillByLabel.bl_idname,
+    #                  icon=FillByLabel.bl_icon, text="")
+
+    # sidebar.separator()
+    # layout.separator()
+
+
+def VIEW3D_TOPBAR(self, context):
+    layout = self.layout
+    layout.operator(SliceViewer.bl_idname,
+                    icon=SliceViewer.bl_icon, text="")
+
+
+node_menu = NodeMenu(
+    menu_items=MENU_ITEMS
+)
+
+
 def add():
-    bpy.types.TOPBAR_MT_file_import.append(TOPBAR_FILE_IMPORT)
-    # bpy.types.TOPBAR_MT_file_export.append(TOPBAR_FILE_EXPORT)
-    bpy.types.OUTLINER_MT_object.append(OUTLINER_OBJECT)
-    bpy.types.VIEW3D_MT_object_context_menu.append(VIEW3D_OBJECT)
+    node_menu.register()
+    bpy.types.VIEW3D_HT_header.append(VIEW3D_TOPBAR)
     bpy.types.TOPBAR_MT_editor_menus.append(TOPBAR)
+    bpy.types.NODE_PT_node_tree_properties.prepend(NODE_PROP)
+    bpy.types.NODE_MT_editor_menus.append(NODE_HEAD)
+    bpy.types.NODE_MT_context_menu.append(NODE_CONTEXT)
 
 
 def remove():
-    bpy.types.TOPBAR_MT_file_import.remove(TOPBAR_FILE_IMPORT)
-    # bpy.types.TOPBAR_MT_file_export.remove(TOPBAR_FILE_EXPORT)
-    bpy.types.OUTLINER_MT_object.remove(OUTLINER_OBJECT)
-    bpy.types.VIEW3D_MT_object_context_menu.remove(VIEW3D_OBJECT)
+    bpy.types.VIEW3D_HT_header.remove(VIEW3D_TOPBAR)
     bpy.types.TOPBAR_MT_editor_menus.remove(TOPBAR)
+    bpy.types.NODE_PT_node_tree_properties.remove(NODE_PROP)
+    bpy.types.NODE_MT_editor_menus.remove(NODE_HEAD)
+    bpy.types.NODE_MT_context_menu.remove(NODE_CONTEXT)
+    node_menu.unregister()

bioxelnodes/node_menu.py

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

bioxelnodes/nodes.py

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

bioxelnodes/operators/container.py

@@ -1,15 +1,17 @@
 import bpy
 
-
 import bmesh
 
-from ..nodes import custom_nodes
+from ..utils import get_cache_dir, get_use_link, select_object
 from ..bioxel.io import load_container, save_container
-from ..bioxelutils.layer import get_all_layer_objs
-from ..bioxelutils.container import (container_to_obj, obj_to_container,
-                                     get_container_objs_from_selection)
-from ..bioxelutils.node import get_nodes_by_type, move_node_between_nodes, move_node_to_node
-from .utils import change_render_setting, get_cache_dir, get_preferences, select_object
+from ..bioxelutils.container import container_to_obj, obj_to_container
+from ..bioxelutils.node import add_node_to_graph
+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
 
 
 class SaveContainer(bpy.types.Operator):
@@ -23,19 +25,14 @@ class SaveContainer(bpy.types.Operator):
 
     filename_ext = ".bioxel"
 
-    @classmethod
-    def poll(cls, context):
-        container_objs = get_container_objs_from_selection()
-        return len(container_objs) > 0
-
     def execute(self, context):
-        container_objs = get_container_objs_from_selection()
+        container_obj = get_container_obj(context.object)
 
-        if len(container_objs) == 0:
+        if container_obj is None:
             self.report({"WARNING"}, "Cannot find any bioxel container.")
             return {'FINISHED'}
 
-        container = obj_to_container(container_objs[0])
+        container = obj_to_container(container_obj)
         save_path = f"{self.filepath.split('.')[0]}.bioxel"
         save_container(container, save_path, overwrite=True)
 
@@ -65,11 +62,12 @@ class LoadContainer(bpy.types.Operator):
 
         container_obj = container_to_obj(container,
                                          scene_scale=0.01,
-                                         cache_dir=get_cache_dir(context))
+                                         cache_dir=get_cache_dir())
         select_object(container_obj)
 
         if is_first_import:
-            change_render_setting(context)
+            bpy.ops.bioxelnodes.render_setting_preset('EXEC_DEFAULT',
+                                                      preset="preview_c")
 
         self.report({"INFO"}, f"Successfully load {load_path}")
         return {'FINISHED'}
@@ -79,39 +77,33 @@ class LoadContainer(bpy.types.Operator):
         return {'RUNNING_MODAL'}
 
 
-class PickObject():
+class ExtractObject():
     bl_options = {'UNDO'}
 
-    @classmethod
-    def poll(cls, context):
-        container_objs = get_container_objs_from_selection()
-        return len(container_objs) > 0
-
     def execute(self, context):
-        container_objs = get_container_objs_from_selection()
+        container_obj = get_container_obj(context.object)
 
-        if len(container_objs) == 0:
+        if container_obj is None:
             self.report({"WARNING"}, "Cannot find any bioxel container.")
             return {'FINISHED'}
 
-        container_obj = container_objs[0]
-
         bpy.ops.mesh.primitive_cube_add(
             size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
         obj = bpy.context.active_object
 
-        obj.name = f"{self.object_type}_{container_obj.name}"
+        obj.name = f"{container_obj.name}_{self.object_type}"
 
         bpy.ops.node.new_geometry_nodes_modifier()
         modifier = obj.modifiers[0]
         node_group = modifier.node_group
 
         output_node = get_nodes_by_type(node_group, 'NodeGroupOutput')[0]
-        pick_mesh_node = custom_nodes.add_node(node_group,
-                                               f"BioxelNodes_Pick{self.object_type}")
+        fetch_mesh_node = add_node_to_graph(f"Fetch{self.object_type}",
+                                            node_group,
+                                            get_use_link())
 
-        pick_mesh_node.inputs[0].default_value = container_obj
-        node_group.links.new(pick_mesh_node.outputs[0], output_node.inputs[0])
+        fetch_mesh_node.inputs[0].default_value = container_obj
+        node_group.links.new(fetch_mesh_node.outputs[0], output_node.inputs[0])
 
         select_object(obj)
 
@@ -120,71 +112,78 @@ class PickObject():
         return {'FINISHED'}
 
 
-class PickMesh(bpy.types.Operator, PickObject):
-    bl_idname = "bioxelnodes.pick_mesh"
-    bl_label = "Pick Mesh"
-    bl_description = "Pick Container Mesh"
-    object_type = "Mesh"
+class ExtractSurface(bpy.types.Operator, ExtractObject):
+    bl_idname = "bioxelnodes.fetch_mesh"
+    bl_label = "Extract Surface"
+    bl_description = "Extract Surface"
+    bl_icon = "OUTLINER_OB_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_description = "Pick Container Volume"
+    bl_label = "Extract 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_description = "Pick Container Bbox Wire"
+    bl_label = "Extract Bbox Wire"
+    bl_description = "Extract Bbox Wire"
+    bl_icon = "MESH_CUBE"
     object_type = "BboxWire"
 
 
 class AddCutter():
     bl_options = {'UNDO'}
 
-    @classmethod
-    def poll(cls, context):
-        container_objs = get_container_objs_from_selection()
-        return len(container_objs) > 0
-
     def execute(self, context):
-        container_objs = get_container_objs_from_selection()
+        container_obj = get_container_obj(context.object)
 
-        if len(container_objs) == 0:
+        if container_obj is None:
             self.report({"WARNING"}, "Cannot find any bioxel container.")
             return {'FINISHED'}
-
-        container_obj = container_objs[0]
-
-        if self.object_type == "plane":
-            node_type = "BioxelNodes_PlaneObjectCutter"
+        # TODO: do not use operator to create obj
+        if self.cutter_type == "plane":
             bpy.ops.mesh.primitive_plane_add(
                 size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-        elif self.object_type == "cylinder":
-            node_type = "BioxelNodes_CylinderObjectCutter"
+        elif self.cutter_type == "cylinder":
             bpy.ops.mesh.primitive_cylinder_add(
                 radius=1, depth=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
             bpy.context.object.rotation_euler[0] = container_obj.rotation_euler[0]
-        elif self.object_type == "cube":
-            node_type = "BioxelNodes_CubeObjectCutter"
+        elif self.cutter_type == "cube":
             bpy.ops.mesh.primitive_cube_add(
                 size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-        elif self.object_type == "sphere":
-            node_type = "BioxelNodes_SphereObjectCutter"
+        elif self.cutter_type == "sphere":
             bpy.ops.mesh.primitive_ico_sphere_add(
                 radius=1, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-        elif self.object_type == "pie":
-            node_type = "BioxelNodes_PieObjectCutter"
+        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_obj = bpy.context.active_object
+            orig_data = pie_obj.data
+
             # Create mesh
             pie_mesh = bpy.data.meshes.new('Pie')
+            pie_obj.data = pie_mesh
+            bpy.data.meshes.remove(orig_data)
 
-            # Create object
-            pie = bpy.data.objects.new('Pie', pie_mesh)
+            # # Create object
+            # pie = bpy.data.objects.new('Pie', pie_mesh)
+
+            # # Link object to scene
+            # bpy.context.scene.collection.objects.link(pie)
 
-            # Link object to scene
-            bpy.context.scene.collection.objects.link(pie)
             # Get a BMesh representation
             bm = bmesh.new()   # create an empty BMesh
             bm.from_mesh(pie_mesh)   # fill it in from a Mesh
@@ -208,9 +207,22 @@ class AddCutter():
 
             # Finish up, write the bmesh back to the mesh
             bm.to_mesh(pie_mesh)
-            bpy.context.view_layer.objects.active = pie
+            # bpy.context.view_layer.objects.active = pie
 
         cutter_obj = bpy.context.active_object
+
+        # vcos = [container_obj.matrix_world @
+        #         v.co for v in container_obj.data.vertices]
+
+        # def find_center(l): return (max(l) + min(l)) / 2
+
+        # x, y, z = [[v[i] for v in vcos] for i in range(3)]
+        # center = [find_center(axis) for axis in [x, y, z]]
+
+        # cutter_obj.location = center
+        name = 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
@@ -219,17 +231,28 @@ class AddCutter():
         cutter_obj.visible_shadow = False
         cutter_obj.hide_render = True
         cutter_obj.display_type = 'WIRE'
+        cutter_obj.lineart.usage = 'EXCLUDE'
+
+        select_object(container_obj)
 
         modifier = container_obj.modifiers[0]
         node_group = modifier.node_group
-        cutter_node = custom_nodes.add_node(node_group, node_type)
-        cutter_node.inputs[0].default_value = cutter_obj
 
         cut_nodes = get_nodes_by_type(node_group,
                                       'BioxelNodes_Cut')
-        output_node = get_nodes_by_type(node_group, 'NodeGroupOutput')[0]
         if len(cut_nodes) == 0:
-            cut_node = custom_nodes.add_node(node_group, 'BioxelNodes_Cut')
+            cutter_node = add_node_to_graph("ObjectCutter",
+                                            node_group,
+                                            get_use_link())
+            cutter_node.inputs[0].default_value = self.cutter_type.capitalize()
+            cutter_node.inputs[1].default_value = cutter_obj
+
+            cut_node = add_node_to_graph("Cut",
+                                         node_group,
+                                         get_use_link())
+
+            output_node = get_nodes_by_type(node_group,
+                                            'NodeGroupOutput')[0]
             if len(output_node.inputs[0].links) == 0:
                 node_group.links.new(cut_node.outputs[0],
                                      output_node.inputs[0])
@@ -247,10 +270,13 @@ class AddCutter():
                                  cut_node.inputs[1])
 
             move_node_to_node(cutter_node, cut_node, (-300, -300))
-            select_object(cutter_obj)
         else:
-            move_node_to_node(cutter_node, output_node, (0, -100))
-            select_object(container_obj)
+            bpy.ops.bioxelnodes.add_node('EXEC_DEFAULT',
+                                         node_name="ObjectCutter",
+                                         node_label=name)
+            node = bpy.context.active_node
+            node.inputs[0].default_value = name
+            node.inputs[1].default_value = cutter_obj
 
         return {'FINISHED'}
 
@@ -258,33 +284,242 @@ class AddCutter():
 class AddPlaneCutter(bpy.types.Operator, AddCutter):
     bl_idname = "bioxelnodes.add_plane_cutter"
     bl_label = "Add a Plane Cutter"
-    bl_description = "Add a Plane Cutter to Container"
-    object_type = "plane"
+    bl_description = "Add a plane cutter to current container"
+    bl_icon = "MESH_PLANE"
+    cutter_type = "plane"
 
 
 class AddCylinderCutter(bpy.types.Operator, AddCutter):
     bl_idname = "bioxelnodes.add_cylinder_cutter"
     bl_label = "Add a Cylinder Cutter"
-    bl_description = "Add a Cylinder Cutter to Container"
-    object_type = "cylinder"
+    bl_description = "Add a cylinder cutter to current container"
+    bl_icon = "MESH_CYLINDER"
+    cutter_type = "cylinder"
 
 
 class AddCubeCutter(bpy.types.Operator, AddCutter):
     bl_idname = "bioxelnodes.add_cube_cutter"
     bl_label = "Add a Cube Cutter"
-    bl_description = "Add a Cube Cutter to Container"
-    object_type = "cube"
+    bl_description = "Add a cube cutter to current container"
+    bl_icon = "MESH_CUBE"
+    cutter_type = "cube"
 
 
 class AddSphereCutter(bpy.types.Operator, AddCutter):
     bl_idname = "bioxelnodes.add_sphere_cutter"
     bl_label = "Add a Sphere Cutter"
-    bl_description = "Add a Sphere Cutter to Container"
-    object_type = "sphere"
+    bl_description = "Add a sphere cutter to current container"
+    bl_icon = "MESH_UVSPHERE"
+    cutter_type = "sphere"
 
 
 class AddPieCutter(bpy.types.Operator, AddCutter):
     bl_idname = "bioxelnodes.add_pie_cutter"
     bl_label = "Add a Pie Cutter"
-    bl_description = "Add a Pie Cutter to Container"
-    object_type = "pie"
+    bl_description = "Add a pie cutter to current container"
+    bl_icon = "MESH_CONE"
+    cutter_type = "pie"
+
+
+class AddSlicer(bpy.types.Operator):
+    bl_idname = "bioxelnodes.add_slicer"
+    bl_label = "Add a Slicer"
+    bl_description = "Add a slicer to current container"
+    bl_icon = "TEXTURE"
+    bl_options = {'UNDO'}
+
+    def execute(self, context):
+        container_obj = get_container_obj(context.object)
+
+        if container_obj is None:
+            self.report({"WARNING"}, "Cannot find any bioxel container.")
+            return {'FINISHED'}
+
+        bpy.ops.mesh.primitive_plane_add(size=2,
+                                         enter_editmode=False,
+                                         align='WORLD',
+                                         location=(0, 0, 0),
+                                         scale=(1, 1, 1))
+
+        slicer_obj = bpy.context.active_object
+        slicer_obj.name = "Slicer"
+        slicer_obj.data.name = "Slicer"
+
+        slicer_obj.visible_camera = False
+        slicer_obj.visible_diffuse = False
+        slicer_obj.visible_glossy = False
+        slicer_obj.visible_transmission = False
+        slicer_obj.visible_volume_scatter = False
+        slicer_obj.visible_shadow = False
+        slicer_obj.hide_render = True
+        slicer_obj.display_type = 'WIRE'
+        slicer_obj.lineart.usage = 'EXCLUDE'
+
+        select_object(container_obj)
+
+        modifier = container_obj.modifiers[0]
+        node_group = modifier.node_group
+
+        slice_node = add_node_to_graph("Slice",
+                                       node_group,
+                                       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",
+                                         soft_min=0.0001, soft_max=10.0,
+                                         min=1e-6, max=1e6,
+                                         default=0.01)  # type: ignore
+
+    step_size: bpy.props.FloatProperty(name="Step Size",
+                                       soft_min=0.1, soft_max=100.0,
+                                       min=0.1, max=1e2,
+                                       default=1)  # type: ignore
+
+    def execute(self, context):
+        container_obj = get_container_obj(context.object)
+
+        if container_obj is None:
+            self.report({"WARNING"}, "Cannot find any bioxel container.")
+            return {'FINISHED'}
+
+        container_obj.scale[0] = self.scene_scale
+        container_obj.scale[1] = self.scene_scale
+        container_obj.scale[2] = self.scene_scale
+        container_obj["scene_scale"] = self.scene_scale
+        container_obj["step_size"] = self.step_size
+
+        for layer_obj in get_container_layer_objs(container_obj):
+            layer_obj.data.render.space = 'WORLD'
+            layer_obj.data.render.step_size = self.scene_scale * self.step_size
+
+        return {'FINISHED'}
+
+    def invoke(self, context, event):
+        container_obj = get_container_obj(context.object)
+
+        if container_obj is None:
+            return self.execute(context)
+        else:
+            self.scene_scale = container_obj.get("scene_scale") or 0.01
+            self.step_size = container_obj.get("step_size") or 1
+            context.window_manager.invoke_props_dialog(self)
+            return {'RUNNING_MODAL'}
+
+
+def get_container_layers(context, layer_filter=None):
+    def _layer_filter(layer_obj, context):
+        return True
+
+    layer_filter = layer_filter or _layer_filter
+    container_obj = context.object
+    layer_objs = get_container_layer_objs(container_obj)
+    return [obj for obj in layer_objs if layer_filter(obj, context)]
+
+
+class SaveContainerLayersCache(bpy.types.Operator, SaveLayersCache):
+    bl_idname = "bioxelnodes.save_container_layers_cache"
+    bl_label = "Save Container Layers' Cache"
+    bl_description = "Save all current container layers' cache to directory."
+    bl_icon = "FILE_TICK"
+
+    success_msg = "Successfully saved all container layers."
+
+    def get_layers(self, context):
+        def is_not_missing(layer_obj, context):
+            return not is_missing_layer(layer_obj)
+        return get_container_layers(context, is_not_missing)
+
+
+class RemoveContainerMissingLayers(bpy.types.Operator, RemoveLayers):
+    bl_idname = "bioxelnodes.remove_container_missing_layers"
+    bl_label = "Remove Container Missing Layers"
+    bl_description = "Remove all current container missing layers"
+    bl_icon = "BRUSH_DATA"
+
+    success_msg = "Successfully removed all container missing layers."
+
+    def get_layers(self, context):
+        def is_missing(layer_obj, context):
+            return is_missing_layer(layer_obj)
+        return get_container_layers(context, is_missing)
+
+    def invoke(self, context, event):
+        context.window_manager.invoke_confirm(self,
+                                              event,
+                                              message=f"Are you sure to remove all **Missing** layers?")
+        return {'RUNNING_MODAL'}

bioxelnodes/operators/io.py

@@ -5,20 +5,20 @@ import threading
 import numpy as np
 from pathlib import Path
 
-
 from ..exceptions import CancelledByUser
 from ..props import BIOXELNODES_Series
-from ..bioxel.layer import Layer
-from ..bioxelutils.layer import (get_all_layer_objs,
-                                 get_layer_obj)
+from ..bioxelutils.common import (get_all_layer_objs, get_container_obj,
+                                  get_layer_obj, is_incompatible)
 from ..bioxelutils.container import (Container,
                                      add_layers,
-                                     container_to_obj,
-                                     get_container_objs_from_selection)
+                                     container_to_obj)
+from ..bioxel.layer import Layer
 from ..bioxel.parse import (DICOM_EXTS, SUPPORT_EXTS,
                             get_ext, parse_volumetric_data)
-from .utils import (change_render_setting, get_cache_dir, get_preferences,
-                    progress_update, progress_bar, select_object)
+
+from ..utils import (get_cache_dir,
+                     progress_update, progress_bar,
+                     select_object)
 
 # 3rd-party
 import SimpleITK as sitk
@@ -57,7 +57,7 @@ class ImportVolumetricData():
 
     filepath: bpy.props.StringProperty(subtype="FILE_PATH")  # type: ignore
 
-    read_as = "scalar"
+    read_as = "SCALAR"
 
     def execute(self, context):
         data_path = Path(self.filepath).resolve()
@@ -78,18 +78,28 @@ class ImportVolumetricData():
         return {'RUNNING_MODAL'}
 
 
-class ImportAsScalarLayer(bpy.types.Operator, ImportVolumetricData):
-    bl_idname = "bioxelnodes.import_as_scalar_layer"
+class ImportAsScalar(bpy.types.Operator, ImportVolumetricData):
+    bl_idname = "bioxelnodes.import_as_scalar"
     bl_label = "Import as Scalar"
     bl_description = "Import Volumetric Data to Container as Scalar"
-    read_as = "scalar"
+    bl_icon = "EVENT_S"
+    read_as = "SCALAR"
 
 
-class ImportAsLabelLayer(bpy.types.Operator, ImportVolumetricData):
-    bl_idname = "bioxelnodes.import_as_label_layer"
+class ImportAsLabel(bpy.types.Operator, ImportVolumetricData):
+    bl_idname = "bioxelnodes.import_as_label"
     bl_label = "Import as Label"
     bl_description = "Import Volumetric Data to Container as Label"
-    read_as = "label"
+    bl_icon = "EVENT_L"
+    read_as = "LABEL"
+
+
+class ImportAsColor(bpy.types.Operator, ImportVolumetricData):
+    bl_idname = "bioxelnodes.import_as_color"
+    bl_label = "Import as Label"
+    bl_description = "Import Volumetric Data to Container as Label"
+    bl_icon = "EVENT_C"
+    read_as = "COLOR"
 
 
 class BIOXELNODES_FH_ImportVolumetricData(bpy.types.FileHandler):
@@ -100,7 +110,16 @@ class BIOXELNODES_FH_ImportVolumetricData(bpy.types.FileHandler):
 
     @classmethod
     def poll_drop(cls, context):
-        return (context.area and context.area.type == 'VIEW_3D')
+        if not context.area:
+            return False
+
+        if context.area.type == 'VIEW_3D':
+            return True
+        elif context.area.type == 'NODE_EDITOR':
+            container_obj = get_container_obj(context.object)
+            return container_obj is not None
+        else:
+            return False
 
 
 def get_series_ids(self, context):
@@ -123,9 +142,10 @@ class ParseVolumetricData(bpy.types.Operator):
     bl_options = {'UNDO'}
 
     meta = None
+    label_count = 0
+    dtype = None
     thread = None
     _timer = None
-    container_obj_name = ""
 
     progress: bpy.props.FloatProperty(name="Progress",
                                       options={"SKIP_SAVE"},
@@ -142,9 +162,10 @@ class ParseVolumetricData(bpy.types.Operator):
                                                options={"SKIP_SAVE"})  # type: ignore
 
     read_as: bpy.props.EnumProperty(name="Read as",
-                                    default="scalar",
-                                    items=[("scalar", "Scalar", ""),
-                                           ("label", "Labels", "")])  # type: ignore
+                                    default="SCALAR",
+                                    items=[("SCALAR", "Scalar", ""),
+                                           ("LABEL", "Labels", ""),
+                                           ("COLOR", "Color", "")])  # type: ignore
 
     series_id: bpy.props.EnumProperty(name="Select Series",
                                       items=get_series_ids)  # type: ignore
@@ -153,6 +174,15 @@ class ParseVolumetricData(bpy.types.Operator):
         type=BIOXELNODES_Series)  # type: ignore
 
     def execute(self, context):
+        if is_incompatible():
+            self.report({"ERROR"},
+                        "Current addon verison is not compatible to this file. If you insist on editing this file please keep the same addon version")
+            return {'CANCELLED'}
+
+        if not self.filepath:
+            self.report({"WARNING"}, "No file selected.")
+            return {'CANCELLED'}
+
         data_path = Path(self.filepath).resolve()
         ext = get_ext(data_path)
         if ext not in SUPPORT_EXTS:
@@ -182,6 +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
@@ -207,7 +239,7 @@ class ParseVolumetricData(bpy.types.Operator):
         # Check if user press 'ESC'
         if event.type == 'ESC':
             self.is_cancelled = True
-            progress_update(context, 0, "Canceling...")
+            progress_update(context, 0.0, "Canceling...")
             return {'PASS_THROUGH'}
 
         # Check if is the timer time
@@ -227,6 +259,7 @@ class ParseVolumetricData(bpy.types.Operator):
         context.window_manager.event_timer_remove(self._timer)
         # Remove the progress bar from status bar
         bpy.types.STATUSBAR_HT_header.remove(progress_bar)
+        progress_update(context, 1.0)
 
         # Check if thread is cancelled by user
         if self.is_cancelled:
@@ -246,25 +279,57 @@ 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']
-        min_size = min(orig_spacing[0],
-                       orig_spacing[1], orig_spacing[2])
-        bioxel_size = max(min_size, 1.0)
 
-        layer_shape = get_layer_shape(1, orig_shape, orig_spacing)
+        min_log10 = math.floor(math.log10(min(*orig_spacing)))
+        max_log10 = math.floor(math.log10(max(*orig_spacing)))
+        # min_space = min(*orig_spacing)
+        # max_space = max(*orig_spacing)
+
+        if orig_spacing[2] == 1 and min_log10 < -1:
+            orig_spacing = (orig_spacing[0] * math.pow(10, -min_log10-2),
+                            orig_spacing[1] * math.pow(10, -min_log10-2),
+                            1)
+        elif min_log10 > 0:
+            orig_spacing = (orig_spacing[0] * math.pow(10, -min_log10-1),
+                            orig_spacing[1] * math.pow(10, -min_log10-1),
+                            orig_spacing[2] * math.pow(10, -min_log10-1))
+        elif max_log10 < 0:
+            orig_spacing = (orig_spacing[0] * math.pow(10, -max_log10-1),
+                            orig_spacing[1] * math.pow(10, -max_log10-1),
+                            orig_spacing[2] * math.pow(10, -max_log10-1))
+
+        bioxel_size = max(min(*orig_spacing), 1.0)
+
+        layer_shape = get_layer_shape(bioxel_size,
+                                      orig_shape,
+                                      orig_spacing)
         layer_size = get_layer_size(layer_shape,
-                                    bioxel_size)
-        log10 = math.floor(math.log10(max(*layer_size)))
-        log10 = max(1, log10)
-        log10 = min(3, log10)
-        scene_scale = math.pow(10, -log10)
+                                    bioxel_size,
+                                    0.01)
+        min_log10 = math.floor(math.log10(min(*layer_size)))
+        max_log10 = math.floor(math.log10(max(*layer_size)))
 
-        if self.container_obj_name:
-            container_obj = bpy.data.objects.get(self.container_obj_name)
+        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":
+            container_obj = context.object
             container_name = container_obj.name
+            container_obj_name = container_name
         else:
             container_name = self.meta['name']
+            container_obj_name = ""
 
         series_id = self.series_id if self.series_id != "empty" else ""
         bpy.ops.bioxelnodes.import_volumetric_data_dialog(
@@ -278,8 +343,9 @@ class ParseVolumetricData(bpy.types.Operator):
             series_id=series_id,
             frame_count=self.meta['frame_count'],
             channel_count=self.meta['channel_count'],
-            container_obj_name=self.container_obj_name,
+            container_obj_name=container_obj_name,
             read_as=self.read_as,
+            label_count=self.label_count,
             scene_scale=scene_scale
         )
 
@@ -287,18 +353,22 @@ class ParseVolumetricData(bpy.types.Operator):
         return {'FINISHED'}
 
     def invoke(self, context, event):
-        if not self.filepath:
+        # why not report in execute?
+        # If this operator is executing, a new execute will when pre-one done.
+        if context.window_manager.bioxelnodes_progress_factor < 1:
+            print("A process is executing, please wait for it to finish.")
             return {'CANCELLED'}
 
+        if not self.filepath:
+            return self.execute(context)
+
         data_path = Path(self.filepath).resolve()
         ext = get_ext(data_path)
 
-        container_objs = get_container_objs_from_selection()
-        if len(container_objs) > 0:
-            self.container_obj_name = container_objs[0].name
-
-        title = f"Add to **{self.container_obj_name}**" \
-            if self.container_obj_name != "" else f"Init a Container"
+        if context.area.type == "NODE_EDITOR":
+            title = f"Add to **{context.object.name}**"
+        else:
+            title = "Init a Container"
 
         # Series Selection
         if ext in DICOM_EXTS:
@@ -367,8 +437,7 @@ class ParseVolumetricData(bpy.types.Operator):
                 return {'CANCELLED'}
 
         if self.skip_read_as:
-            self.execute(context)
-            return {'RUNNING_MODAL'}
+            return self.execute(context)
         else:
             context.window_manager.invoke_props_dialog(self,
                                                        width=400,
@@ -386,17 +455,17 @@ class ParseVolumetricData(bpy.types.Operator):
             layout.prop(self, "series_id")
 
 
-def get_sequence_sources(self, context):
-    items = [("-1", "None (1 frame)", "")]
+def get_frame_sources(self, context):
+    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(("2", f"Y ({orig_shape[1]} frames)", ""))
-        items.append(("3", f"Z ({orig_shape[2]} frames)", ""))
+        items.append(("1", f"X-axis ({orig_shape[0]} frames)", ""))
+        items.append(("2", f"Y-axis ({orig_shape[1]} frames)", ""))
+        items.append(("3", f"Z-axis ({orig_shape[2]} frames)", ""))
 
     return items
 
@@ -426,10 +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",
-                                    items=[("scalar", "Scalar", ""),
-                                           ("label", "Labels", "")])  # type: ignore
+                                    default="SCALAR",
+                                    items=[("SCALAR", "Scalar", ""),
+                                           ("LABEL", "Labels", ""),
+                                           ("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,
@@ -447,11 +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",
-                                           default=False)  # type: ignore
+    remap: bpy.props.BoolProperty(name="Remap to 0~1",
+                                  default=False)  # type: ignore
 
-    sequence_source: bpy.props.EnumProperty(name="Time Sequence From",
-                                            items=get_sequence_sources)  # type: ignore
+    split_channel: bpy.props.BoolProperty(name="Split Channels",
+                                          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):
@@ -481,26 +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)
@@ -516,6 +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 = []
@@ -540,12 +616,13 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
                     try:
                         layer = Layer(data=data == np.full_like(data, i+1),
                                       name=name_i,
-                                      kind=kind,
-                                      affine=affine)
+                                      kind=kind)
 
                         layer.resize(shape=shape,
                                      progress_callback=progress_callback)
 
+                        layer.affine = affine
+
                         layers.append(layer)
                     except CancelledByUser:
                         return
@@ -553,10 +630,82 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
                         self.has_error = e
                         return
 
+            if kind == "color":
+                if np.issubdtype(np.uint8, data.dtype):
+                    data = np.multiply(data, 1.0 / 256,
+                                       dtype=np.float32)
+                elif data.dtype.kind in ['u', 'i']:
+                    # Convert the normalized array to float dtype
+                    data = data.astype(np.float32)
+
+                    min_val = data.min()
+                    max_val = data.max()
+                    # Avoid division by zero if all values are the same
+                    if max_val != min_val:
+                        # Normalize the array to the range (0,1)
+                        data = (data - min_val) / (max_val - min_val)
+                    else:
+                        # If all values are the same, the normalized array will be all zeros
+                        data = np.zeros_like(data, dtype=np.float32)
+
+                else:
+                    data = data.astype(np.float32)
+
+                name = self.layer_name or "Color"
+                if data.shape[4] == 1:
+                    data = np.repeat(data, repeats=3, axis=4)
+                elif data.shape[4] == 2:
+                    d_shape = list(data.shape)
+                    d_shape = d_shape[:4] + [1]
+                    zore = np.zeros(tuple(d_shape), dtype=np.float32)
+                    data = np.concatenate((data, zore), axis=-1)
+                elif data.shape[4] > 3:
+                    data = data[:, :, :, :, :3]
+
+                if cancel():
+                    return
+
+                progress_update(context, 0.2,
+                                f"Processing {name}...")
+                progress_callback = progress_callback_factory(name,
+                                                              0.2,
+                                                              0.7)
+
+                try:
+                    layer = Layer(data=data,
+                                  name=name,
+                                  kind=kind)
+
+                    layer.resize(shape=shape,
+                                 progress_callback=progress_callback)
+
+                    layer.affine = affine
+
+                    layers.append(layer)
+                except CancelledByUser:
+                    return
+                except Exception as e:
+                    self.has_error = e
+                    return
+
             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):
@@ -573,12 +722,13 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
                         try:
                             layer = Layer(data=data[:, :, :, :, i:i+1],
                                           name=name_i,
-                                          kind=kind,
-                                          affine=affine)
+                                          kind=kind)
 
                             layer.resize(shape=shape,
                                          progress_callback=progress_callback)
 
+                            layer.affine = affine
+
                             layers.append(layer)
                         except CancelledByUser:
                             return
@@ -598,12 +748,13 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
                     try:
                         layer = Layer(data=data,
                                       name=name,
-                                      kind=kind,
-                                      affine=affine)
+                                      kind=kind)
 
                         layer.resize(shape=shape,
                                      progress_callback=progress_callback)
 
+                        layer.affine = affine
+
                         layers.append(layer)
                     except CancelledByUser:
                         return
@@ -634,7 +785,7 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
     def modal(self, context, event):
         if event.type == 'ESC':
             self.is_cancelled = True
-            progress_update(context, 0, "Canceling...")
+            progress_update(context, 0.0, "Canceling...")
             return {'PASS_THROUGH'}
 
         if event.type != 'TIMER':
@@ -647,6 +798,7 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
         self.thread.join()
         context.window_manager.event_timer_remove(self._timer)
         bpy.types.STATUSBAR_HT_header.remove(progress_bar)
+        progress_update(context, 1.0)
 
         if self.is_cancelled:
             self.report({"WARNING"}, "Canncelled by user.")
@@ -670,20 +822,25 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
 
             container_obj = add_layers(self.layers,
                                        container_obj=container_obj,
-                                       cache_dir=get_cache_dir(context))
+                                       cache_dir=get_cache_dir())
         else:
-            container = Container(name=self.container_name,
+            name = self.container_name or "Container"
+            container = Container(name=name,
                                   layers=self.layers)
 
+            step_size = container.layers[0].bioxel_size[0]*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)
 
         # Change render setting for better result
         if is_first_import:
-            change_render_setting(context)
+            bpy.ops.bioxelnodes.render_setting_preset('EXEC_DEFAULT',
+                                                      preset="preview_c")
+            # bpy.ops.bioxelnodes.slice_viewer('EXEC_DEFAULT')
 
         self.report({"INFO"}, "Successfully Imported")
         return {'FINISHED'}
@@ -706,54 +863,69 @@ 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!**"
 
+        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 == "":
-            layout.prop(self, "container_name")
-        layout.prop(self, "layer_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.label(text=layer_shape_text)
+        panel.prop(self, "frame_source")
 
-        panel = layout.box()
-        panel.prop(self, "sequence_source")
+        if self.read_as == "SCALAR":
+            panel.prop(self, "split_channel",
+                       text=f"Split Channel as Multi Layer")
 
-        if self.read_as == "scalar":
-            panel = layout.box()
-            panel.prop(self, "split_channels",
-                       text=f"Split Channels (Get {channel_count} channels, import {import_channel} channels)")
-
-        if self.container_obj_name == "":
-            layer_size = get_layer_size(layer_shape,
-                                        self.bioxel_size,
-                                        self.scene_scale)
-            layer_size_text = f"Size will be: ({layer_size[0]:.2f}, {layer_size[1]:.2f}, {layer_size[2]:.2f}) m"
-            panel = layout.box()
-            panel.prop(self, "scene_scale")
-            panel.label(text=layer_size_text)
+        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):

bioxelnodes/operators/layer.py

@@ -3,21 +3,14 @@ import bpy
 
 import numpy as np
 
-
+from ..exceptions import NoContent
 from ..bioxel.layer import Layer
-from ..bioxelutils.node import get_nodes_by_type
-from ..bioxelutils.container import add_layers, get_container_obj
-from ..bioxelutils.layer import obj_to_layer, get_container_layer_objs, get_layer_obj
-from .utils import get_preferences, select_object
-
-
-def get_layer_prop_value(layer_obj: bpy.types.Object, prop: str):
-    try:
-        node_group = layer_obj.modifiers[0].node_group
-        layer_node = get_nodes_by_type(node_group, "BioxelNodes__Layer")[0]
-        return layer_node.inputs[prop].default_value
-    except:
-        return None
+from ..bioxelutils.common import (get_container_obj, get_layer_kind, get_layer_label, get_layer_name,
+                                  get_layer_prop_value,
+                                  get_container_layer_objs,
+                                  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, copy_to_dir
 
 
 def get_label_layer_selection(self, context):
@@ -25,86 +18,327 @@ def get_label_layer_selection(self, context):
     container_obj = get_container_obj(bpy.context.active_object)
 
     for layer_obj in get_container_layer_objs(container_obj):
-        if get_layer_prop_value(layer_obj, "kind") == "label":
+        kind = get_layer_prop_value(layer_obj, "kind")
+        name = get_layer_prop_value(layer_obj, "name")
+        if kind == "label":
             items.append((layer_obj.name,
-                          layer_obj.name,
+                          name,
                           ""))
 
     return items
 
 
-class LayerOperator():
+class FetchLayer(bpy.types.Operator):
+    bl_idname = "bioxelnodes.fetch_layer"
+    bl_label = "Fetch Layer"
+    bl_description = "Fetch layer from current container"
+    bl_icon = "NODE"
     bl_options = {'UNDO'}
-    base_obj: bpy.types.Object = None
 
-    def add_layer(self, context, layer):
-        preferences = get_preferences(context)
-        cache_dir = Path(preferences.cache_dir, 'VDBs')
-        container_obj = self.base_obj.parent
+    layer_obj_name: bpy.props.StringProperty(
+        options={"HIDDEN"})  # type: ignore
 
-        add_layers([layer],
-                   container_obj,
-                   cache_dir)
-
-        select_object(container_obj)
-
-    def invoke(self, context, event):
-        self.base_obj = get_layer_obj(bpy.context.active_object)
-        return self.execute(context)
-
-
-class ScalarOperator(LayerOperator):
     @classmethod
-    def poll(cls, context):
-        label_objs = [obj for obj in context.selected_ids
-                      if get_layer_prop_value(obj, "kind") == "scalar"]
-        return True if len(label_objs) > 0 else False
+    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"]])
 
-
-class LabelOperator(LayerOperator):
-    @classmethod
-    def poll(cls, context):
-        label_objs = [obj for obj in context.selected_ids
-                      if get_layer_prop_value(obj, "kind") == "label"]
-        return True if len(label_objs) > 0 else False
-
-
-class SignScalar(bpy.types.Operator, ScalarOperator):
-    bl_idname = "bioxelnodes.sign_scalar"
-    bl_label = "Sign Scalar"
-    bl_description = "Sign the scalar value"
+    @property
+    def layer_obj(self):
+        return bpy.data.objects.get(self.layer_obj_name)
 
     def execute(self, context):
-        base_layer = obj_to_layer(self.base_obj)
+        if self.layer_obj == None:
+            self.report({"WARNING"}, "Get no layer.")
+            return {'FINISHED'}
 
-        modified_layer = base_layer.copy()
-        modified_layer.data = -base_layer.data
-        modified_layer.name = f"{base_layer.name}_Signed"
+        if is_missing_layer(self.layer_obj):
+            self.report({"WARNING"}, "Selected layer is lost.")
+            return {'FINISHED'}
 
-        self.add_layer(context, modified_layer)
+        bpy.ops.bioxelnodes.add_node('EXEC_DEFAULT',
+                                     node_name="FetchLayer",
+                                     node_label="Fetch Layer")
+        node = bpy.context.active_node
+
+        node.inputs[0].default_value = self.layer_obj
+        node.label = get_layer_label(self.layer_obj)
+
+        return {"FINISHED"}
+
+
+def get_selected_layers(context, layer_filter=None):
+    def _layer_filter(layer_obj, context):
+        return True
+
+    layer_filter = layer_filter or _layer_filter
+    select_objs = []
+    # node_group = context.space_data.edit_tree
+    for node in context.selected_nodes:
+        if get_node_type(node) == "BioxelNodes_FetchLayer":
+            layer_obj = node.inputs[0].default_value
+            if layer_obj is not None:
+                if layer_filter(layer_obj, context):
+                    select_objs.append(layer_obj)
+
+    return list(set(select_objs))
+
+
+def get_selected_layer(context, layer_filter=None):
+    layer_objs = get_selected_layers(context, layer_filter)
+    return layer_objs[0] if len(layer_objs) > 0 else None
+
+
+class OutputLayerOperator():
+    new_layer_name: bpy.props.StringProperty(name="New Name",
+                                             options={"SKIP_SAVE"})  # type: ignore
+
+    def operate(self, orig_layer: Layer, context):
+        """do the operation"""
+        return orig_layer
+
+    def add_layer_node(self, context, layer):
+        layer_obj = layer_to_obj(layer,
+                                 container_obj=context.object,
+                                 cache_dir=get_cache_dir())
+
+        bpy.ops.bioxelnodes.fetch_layer('INVOKE_DEFAULT',
+                                        layer_obj_name=layer_obj.name)
+
+    def execute(self, context):
+        layer_obj = get_selected_layer(context)
+        if layer_obj == None:
+            self.report({"WARNING"}, "Get no layer.")
+            return {'FINISHED'}
+
+        if is_missing_layer(layer_obj):
+            self.report({"WARNING"}, "Selected layer is lost.")
+            return {'FINISHED'}
+
+        orig_layer = obj_to_layer(layer_obj)
+        try:
+            new_layer = self.operate(orig_layer, context)
+        except NoContent as e:
+            self.report({"WARNING"}, e.message)
+            return {'FINISHED'}
+
+        self.add_layer_node(context, new_layer)
         return {'FINISHED'}
 
 
-class FillOperator(ScalarOperator):
+class LayerOperator():
+
+    def operate(self, layer_obj: bpy.types.Object, context):
+        """do the operation"""
+        ...
+
+    def execute(self, context):
+        layer_obj = get_selected_layer(context)
+        if layer_obj == None:
+            self.report({"WARNING"}, "Get no layer.")
+            return {'FINISHED'}
+
+        if is_missing_layer(layer_obj):
+            self.report({"WARNING"}, "Selected layer is lost.")
+            return {'FINISHED'}
+
+        self.operate(layer_obj, context)
+
+        return {'FINISHED'}
+
+
+class RetimeLayer(bpy.types.Operator, LayerOperator):
+    bl_idname = "bioxelnodes.retime_layer"
+    bl_label = "Retime Sequence"
+    bl_description = "Retime layer time sequence"
+    bl_icon = "TIME"
+
+    frame_duration: bpy.props.IntProperty(name="Frames")  # type: ignore
+    frame_start: bpy.props.IntProperty(name="Start")  # type: ignore
+    frame_offset: bpy.props.IntProperty(name="Offset")  # type: ignore
+    sequence_mode: bpy.props.EnumProperty(name="Mode",
+                                          default="REPEAT",
+                                          items=[("CLIP", "Clip", ""),
+                                                 ("EXTEND", "Extend", ""),
+                                                 ("REPEAT", "Repeat", ""),
+                                                 ("PING_PONG", "Ping-Pong", "")])  # type: ignore
+
+    def operate(self, layer_obj, context):
+        layer_obj.data.frame_duration = self.frame_duration
+        layer_obj.data.frame_start = self.frame_start
+        layer_obj.data.frame_offset = self.frame_offset
+        layer_obj.data.sequence_mode = self.sequence_mode
+
     def invoke(self, context, event):
-        self.base_obj = get_layer_obj(bpy.context.active_object)
-        scalar_min = get_layer_prop_value(self.base_obj, "min")
-        self.fill_value = min(scalar_min, 0)
-        context.window_manager.invoke_props_dialog(self, width=400)
-        return {'RUNNING_MODAL'}
+        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 FillByThreshold(bpy.types.Operator, FillOperator):
-    bl_idname = "bioxelnodes.fill_by_threshold"
-    bl_label = "Fill Value by Threshold"
-    bl_description = "Fill Value by Threshold"
+class RelocateLayer(bpy.types.Operator, LayerOperator):
+    bl_idname = "bioxelnodes.relocate_layer"
+    bl_label = "Relocate Layer Cache"
+    bl_description = "Relocate layer cache"
+    bl_icon = "FILE"
 
-    threshold: bpy.props.FloatProperty(
-        name="Threshold",
-        soft_min=0, soft_max=1024,
-        default=128,
+    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,
+        default=1,
     )  # type: ignore
 
+    @staticmethod
+    def get_new_shape(orig_shape, orig_size, new_size):
+        return (int(orig_shape[0]*orig_size/new_size),
+                int(orig_shape[1]*orig_size/new_size),
+                int(orig_shape[2]*orig_size/new_size))
+
+    def operate(self, orig_layer: Layer, context):
+        new_layer = orig_layer.copy()
+        new_shape = self.get_new_shape(new_layer.shape,
+                                       new_layer.bioxel_size[0],
+                                       self.bioxel_size)
+
+        new_layer.resize(new_shape, self.smooth)
+        new_layer.name = self.new_layer_name \
+            or f"{orig_layer.name}_R-{self.bioxel_size:.2f}"
+        return new_layer
+
+    def draw(self, context):
+        layer_obj = get_selected_layer(context)
+        orig_shape = get_layer_prop_value(layer_obj, "shape")
+        orig_size = get_layer_prop_value(layer_obj, "bioxel_size")
+        new_shape = self.get_new_shape(orig_shape,
+                                       orig_size,
+                                       self.bioxel_size)
+
+        orig_shape = tuple(orig_shape)
+        bioxel_count = new_shape[0] * new_shape[1] * new_shape[2]
+
+        layer_shape_text = f"Shape from {str(orig_shape)} to {str(new_shape)}"
+        if bioxel_count > 100000000:
+            layer_shape_text += "**TOO LARGE!**"
+
+        layout = self.layout
+        layout.prop(self, "new_layer_name")
+        layout.prop(self, "bioxel_size")
+        layout.prop(self, "smooth")
+        layout.label(text=layer_shape_text)
+
+    def invoke(self, context, event):
+        layer_obj = get_selected_layer(context)
+        if layer_obj:
+            name = get_layer_label(layer_obj)
+            self.bioxel_size = get_layer_prop_value(layer_obj,
+                                                    "bioxel_size")
+            context.window_manager.invoke_props_dialog(self,
+                                                       title=f"Resample {name}")
+            return {'RUNNING_MODAL'}
+        else:
+            return self.execute(context)
+
+
+class SignScalar(bpy.types.Operator, OutputLayerOperator):
+    bl_idname = "bioxelnodes.sign_scalar"
+    bl_label = "Sign Value"
+    bl_description = "Sign value"
+    bl_icon = "REMOVE"
+
+    def operate(self, orig_layer: Layer, context):
+        new_layer = orig_layer.copy()
+        new_layer.data = -orig_layer.data
+        new_layer.name = self.new_layer_name \
+            or f"{orig_layer.name}_Sign"
+        return new_layer
+
+    def invoke(self, context, event):
+        layer_obj = get_selected_layer(context)
+        if layer_obj:
+            name = get_layer_label(layer_obj)
+            context.window_manager.invoke_props_dialog(self,
+                                                       title=f"Sign {name}")
+            return {'RUNNING_MODAL'}
+        else:
+            return self.execute(context)
+
+
+class FillOperator(OutputLayerOperator):
+
     fill_value: bpy.props.FloatProperty(
         name="Fill Value",
         soft_min=0, soft_max=1024.0,
@@ -112,30 +346,52 @@ class FillByThreshold(bpy.types.Operator, FillOperator):
     )  # type: ignore
 
     invert: bpy.props.BoolProperty(
-        name="Invert Area",
+        name="Invert Aera",
         default=True,
     )  # type: ignore
 
-    def execute(self, context):
-        base_layer = obj_to_layer(self.base_obj)
+    def invoke(self, context, event):
+        layer_obj = get_selected_layer(context)
+        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,
+                                                       title=f"Fill {name}")
+            return {'RUNNING_MODAL'}
+        else:
+            return self.execute(context)
 
-        data = np.amax(base_layer.data, -1)
+
+class FillByThreshold(bpy.types.Operator, FillOperator):
+    bl_idname = "bioxelnodes.fill_by_threshold"
+    bl_label = "Fill Value by Threshold"
+    bl_description = "Fill value by threshold"
+    bl_icon = "EMPTY_SINGLE_ARROW"
+
+    threshold: bpy.props.FloatProperty(
+        name="Threshold",
+        soft_min=0, soft_max=1024,
+        default=128,
+    )  # type: ignore
+
+    def operate(self, orig_layer: Layer, context):
+        data = np.amax(orig_layer.data, -1)
         mask = data <= self.threshold \
             if self.invert else data > self.threshold
 
-        modified_layer = base_layer.copy()
-        modified_layer.fill(self.fill_value, mask)
-        modified_layer.name = f"{base_layer.name}_{self.threshold}-Filled"
-
-        self.add_layer(context, modified_layer)
-
-        return {'FINISHED'}
+        new_layer = orig_layer.copy()
+        new_layer.fill(self.fill_value, mask, 3)
+        new_layer.name = self.new_layer_name \
+            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(
         name="From Min",
@@ -149,102 +405,200 @@ class FillByRange(bpy.types.Operator, FillOperator):
         default=256,
     )  # type: ignore
 
-    fill_value: bpy.props.FloatProperty(
-        name="Fill Value",
-        soft_min=0, soft_max=1024.0,
-        default=0,
-    )  # type: ignore
-
-    invert: bpy.props.BoolProperty(
-        name="Invert Area",
-        default=True,
-    )  # type: ignore
-
-    def execute(self, context):
-        base_layer = obj_to_layer(self.base_obj)
-
-        data = np.amax(base_layer.data, -1)
+    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 = base_layer.copy()
-        modified_layer.fill(self.fill_value, mask)
-        modified_layer.name = f"{base_layer.name}_{self.from_min}-{self.from_max}-Filled"
-
-        self.add_layer(context, modified_layer)
-        return {'FINISHED'}
+        new_layer = orig_layer.copy()
+        new_layer.fill(self.fill_value, mask, 3)
+        new_layer.name = self.new_layer_name \
+            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"
 
-    label_obj_name: bpy.props.EnumProperty(
-        name="Label Layer",
-        items=get_label_layer_selection
-    )  # type: ignore
+    smooth: bpy.props.IntProperty(name="Smooth Iteration",
+                                  default=0,
+                                  soft_min=0, soft_max=5,
+                                  options={"SKIP_SAVE"})  # type: ignore
 
-    fill_value: bpy.props.FloatProperty(
-        name="Fill Value",
-        soft_min=0, soft_max=1024.0,
-        default=0,
-    )  # type: ignore
+    label_obj_name: bpy.props.EnumProperty(name="Label Layer",
+                                           items=get_label_layer_selection)  # type: ignore
 
-    invert: bpy.props.BoolProperty(
-        name="Invert Label",
-        default=True,
-    )  # type: ignore
-
-    def execute(self, context):
+    def operate(self, orig_layer: Layer, context):
         label_obj = bpy.data.objects.get(self.label_obj_name)
-        if not label_obj:
-            self.report({"WARNING"}, "Cannot find any label layer.")
-            return {'FINISHED'}
-
-        base_layer = obj_to_layer(self.base_obj)
+        if label_obj is None:
+            raise NoContent("Cannot find any label layer.")
 
         label_layer = obj_to_layer(label_obj)
-        label_layer.resize(base_layer.shape)
+        label_layer.resize(orig_layer.shape, self.smooth)
         mask = np.amax(label_layer.data, -1)
         if self.invert:
             mask = 1 - mask
 
-        modified_layer = base_layer.copy()
-        modified_layer.fill(self.fill_value, mask)
-        modified_layer.name = f"{base_layer.name}_{label_layer.name}-Filled"
-
-        self.add_layer(context, modified_layer)
-        return {'FINISHED'}
+        new_layer = orig_layer.copy()
+        new_layer.fill(self.fill_value, mask, 3)
+        new_layer.name = self.new_layer_name \
+            or f"{orig_layer.name}_F-{label_layer.name}"
+        return new_layer
 
 
-class CombineLabels(bpy.types.Operator, LabelOperator):
+class CombineLabels(bpy.types.Operator, OutputLayerOperator):
     bl_idname = "bioxelnodes.combine_labels"
     bl_label = "Combine Labels"
     bl_description = "Combine all selected labels"
+    bl_icon = "MOD_BUILD"
 
     def execute(self, context):
-        label_objs = [obj for obj in context.selected_ids
-                      if get_layer_prop_value(obj, "kind") == "label"]
+        def layer_filter(layer_obj, context):
+            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(modified_layer.data, label_layer.data)
+            new_layer.data = np.maximum(
+                new_layer.data, label_layer.data)
             label_names.append(label_layer.name)
 
-        modified_layer.name = f"{'-'.join(label_names)}-Combined"
+        new_layer.name = self.new_layer_name \
+            or f"C-{'-'.join(label_names)}"
 
-        self.add_layer(context, modified_layer)
+        self.add_layer_node(context, new_layer)
+        return {'FINISHED'}
+
+
+class BatchLayerOperator():
+    success_msg = "Successfully done selected layers."
+    fail_msg = "fails."
+
+    def execute(self, context):
+        layer_objs = self.get_layers(context)
+
+        fails = []
+        for layer_obj in layer_objs:
+            try:
+                self.operate(layer_obj, context)
+            except:
+                fails.append(layer_obj)
+
+        if len(fails) == 0:
+            self.report({"INFO"}, self.success_msg)
+        else:
+            self.report(
+                {"WARNING"}, f"{','.join([layer_obj.name for layer_obj in fails])} {self.fail_msg}")
 
         return {'FINISHED'}
+
+
+class SaveLayersCache(BatchLayerOperator):
+    fail_msg = "fail to save."
+
+    cache_dir: bpy.props.StringProperty(
+        name="Cache Directory",
+        subtype='DIR_PATH',
+        default="//"
+    )  # type: ignore
+
+    def operate(self, layer_obj, context):
+        output_dir = bpy.path.abspath(self.cache_dir)
+        source_dir = bpy.path.abspath(layer_obj.data.filepath)
+
+        source_path: Path = Path(source_dir).resolve()
+        is_sequence = layer_obj.data.is_sequence
+
+        name = layer_obj.name if is_sequence else f"{layer_obj.name}.vdb"
+        output_path: Path = Path(output_dir, name, source_path.name).resolve() \
+            if is_sequence else Path(output_dir, name).resolve()
+
+        if output_path != source_path:
+            copy_to_dir(source_path.parent if is_sequence else source_path,
+                        output_path.parent.parent if is_sequence else output_path.parent,
+                        new_name=name)
+
+        blend_path = Path(bpy.path.abspath("//")).resolve()
+
+        layer_obj.data.filepath = bpy.path.relpath(str(output_path),
+                                                   start=str(blend_path))
+
+        return {'FINISHED'}
+
+    def invoke(self, context, event):
+        context.window_manager.invoke_props_dialog(self)
+        return {'RUNNING_MODAL'}
+
+
+class RemoveLayers(BatchLayerOperator):
+    fail_msg = "fail to remove."
+
+    def operate(self, layer_obj, context):
+        for node_group in bpy.data.node_groups:
+            for node in node_group.nodes:
+                if get_node_type(node) == "BioxelNodes_FetchLayer":
+                    if node.inputs[0].default_value == layer_obj:
+                        node_group.nodes.remove(node)
+
+        cache_filepath = Path(bpy.path.abspath(
+            layer_obj.data.filepath)).resolve()
+
+        if cache_filepath.is_file():
+            if layer_obj.data.is_sequence:
+                for f in cache_filepath.parent.iterdir():
+                    f.unlink(missing_ok=True)
+            else:
+                cache_filepath.unlink(missing_ok=True)
+
+        # also remove layer object
+        bpy.data.volumes.remove(layer_obj.data)
+
+        return {'FINISHED'}
+
+    def invoke(self, context, event):
+        context.window_manager.invoke_confirm(self,
+                                              event,
+                                              message=f"Are you sure to remove them?")
+        return {'RUNNING_MODAL'}
+
+
+class SaveSelectedLayersCache(bpy.types.Operator, SaveLayersCache):
+    bl_idname = "bioxelnodes.save_selected_layers_cache"
+    bl_label = "Save Selected Layers Cache"
+    bl_description = "Save selected layers' Cache"
+    bl_icon = "FILE_TICK"
+
+    success_msg = "Successfully saved all selected layers."
+
+    def get_layers(self, context):
+        def is_not_missing(layer_obj, context):
+            return not is_missing_layer(layer_obj)
+        return get_selected_layers(context, is_not_missing)
+
+
+class RemoveSelectedLayers(bpy.types.Operator, RemoveLayers):
+    bl_idname = "bioxelnodes.remove_selected_layers"
+    bl_label = "Remove Selected Layers"
+    bl_description = "Remove selected layers"
+    bl_icon = "TRASH"
+
+    success_msg = "Successfully removed all selected layers."
+
+    def get_layers(self, context):
+        return get_selected_layers(context)

bioxelnodes/operators/misc.py

@@ -1,81 +1,51 @@
-import re
 import bpy
 from pathlib import Path
 import shutil
 
+from ..bioxelutils.common import get_all_layer_objs, is_missing_layer, set_file_prop
+from .layer import RemoveLayers, SaveLayersCache
 
-from ..utils import copy_to_dir
-from .utils import get_cache_dir
-from ..nodes import custom_nodes
-from ..bioxelutils.container import get_container_objs_from_selection
-from ..bioxelutils.layer import get_all_layer_objs, get_container_layer_objs
-
-CLASS_PREFIX = "BIOXELNODES_MT_NODES"
+from ..constants import NODE_LIB_FILEPATH, VERSION
+from ..utils import get_cache_dir
 
 
-class ReLinkNodes(bpy.types.Operator):
-    bl_idname = "bioxelnodes.relink_nodes"
-    bl_label = "Relink Nodes to Addon"
-    bl_description = "Relink all nodes to addon source"
+class ReLinkNodeLib(bpy.types.Operator):
+    bl_idname = "bioxelnodes.relink_node_lib"
+    bl_label = "Relink Node Library"
+    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
-        for lib in bpy.data.libraries:
-            lib_path = Path(bpy.path.abspath(lib.filepath)).resolve()
-            lib_name = lib_path.name
-            if lib_name == file_name:
-                if str(lib_path) != custom_nodes.nodes_file:
-                    lib.filepath = custom_nodes.nodes_file
+        lib_filepath = Path(NODE_LIB_FILEPATH.parent,
+                            f"{self.node_lib_filename}.blend")
+        node_libs = []
+        for node_group in bpy.data.node_groups:
+            if node_group.name.startswith("BioxelNodes"):
+                node_lib = node_group.library
+                if node_lib:
+                    node_libs.append(node_lib)
+
+        node_libs = list(set(node_libs))
+
+        for node_lib in node_libs:
+            node_lib.filepath = str(lib_filepath)
+            # FIXME: may cause crash
+            node_lib.reload()
 
         self.report({"INFO"}, f"Successfully relinked.")
 
         return {'FINISHED'}
 
 
-def save_layer_cache(layer_obj, output_dir):
-    pattern = r'\.\d{4}\.'
-
-    # "//"
-    output_dir = bpy.path.abspath(output_dir)
-    source_dir = bpy.path.abspath(layer_obj.data.filepath)
-
-    source_path: Path = Path(source_dir).resolve()
-    is_sequence = re.search(pattern, source_path.name) is not None
-    name = layer_obj.name if is_sequence else f"{layer_obj.name}.vdb"
-    output_path: Path = Path(output_dir, name, source_path.name).resolve() \
-        if is_sequence else Path(output_dir, name).resolve()
-
-    if output_path != source_path:
-        copy_to_dir(source_path.parent if is_sequence else source_path,
-                    output_path.parent.parent if is_sequence else output_path.parent,
-                    new_name=name)
-
-    blend_path = Path(bpy.path.abspath("//")).resolve()
-
-    layer_obj.data.filepath = bpy.path.relpath(
-        str(output_path), start=str(blend_path))
-
-
-class SaveStagedData(bpy.types.Operator):
-    bl_idname = "bioxelnodes.save_staged_data"
-    bl_label = "Save Staged Data"
-    bl_description = "Save all staged data in this file for sharing"
-
-    save_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
+class SaveNodeLib(bpy.types.Operator):
+    bl_idname = "bioxelnodes.save_node_lib"
+    bl_label = "Save Node Library"
+    bl_description = "Save node library file to local"
+    bl_options = {'UNDO'}
 
     lib_dir: bpy.props.StringProperty(
         name="Library Directory",
@@ -84,132 +54,185 @@ 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))
+        lib_dir = bpy.path.abspath(self.lib_dir)
+        local_lib_path: Path = Path(lib_dir, NODE_LIB_FILEPATH.name).resolve()
+        addon_lib_path: Path = NODE_LIB_FILEPATH
+        blend_path = Path(bpy.path.abspath("//")).resolve()
 
-            for file in files:
-                file_name = Path(file).name
-                # "//"
-                lib_dir = bpy.path.abspath(self.lib_dir)
+        if local_lib_path != addon_lib_path:
+            shutil.copy(addon_lib_path, local_lib_path)
 
-                output_path: Path = Path(lib_dir, file_name).resolve()
-                source_path: Path = Path(file).resolve()
+        libs = []
+        for node_group in bpy.data.node_groups:
+            if node_group.name.startswith("BioxelNodes"):
+                if node_group.library:
+                    libs.append(node_group.library)
 
-                if output_path != source_path:
-                    shutil.copy(source_path, output_path)
+        libs = list(set(libs))
+        for lib in libs:
+            lib.filepath = bpy.path.relpath(str(local_lib_path),
+                                            start=str(blend_path))
 
-                for lib in bpy.data.libraries:
-                    lib_path = Path(bpy.path.abspath(lib.filepath)).resolve()
-                    if lib_path == source_path:
-                        blend_path = Path(bpy.path.abspath("//")).resolve()
-                        lib.filepath = bpy.path.relpath(
-                            str(output_path), start=str(blend_path))
-
-                self.report({"INFO"}, f"Successfully saved to {output_path}")
-
-        if self.save_cache:
-            fails = []
-            for layer in get_all_layer_objs():
-                try:
-                    save_layer_cache(layer, self.cache_dir)
-                except:
-                    fails.append(layer)
-
-            if len(fails) == 0:
-                self.report({"INFO"}, f"Successfully saved bioxel layers.")
-            else:
-                self.report(
-                    {"WARNING"}, f"{','.join([layer.name for layer 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,
-                                                   width=500)
+        context.window_manager.invoke_props_dialog(self)
         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 SaveCaches(bpy.types.Operator):
-    bl_idname = "bioxelnodes.save_caches"
-    bl_label = "Save Caches"
-    bl_description = "Save Container's caches to directory."
-
-    cache_dir: bpy.props.StringProperty(
-        name="Layer Directory",
-        subtype='DIR_PATH',
-        default="//"
-    )  # type: ignore
-
-    @classmethod
-    def poll(cls, context):
-        container_objs = get_container_objs_from_selection()
-        return len(container_objs) > 0
+class CleanTemp(bpy.types.Operator):
+    bl_idname = "bioxelnodes.clear_temp"
+    bl_label = "Clean Temp"
+    bl_description = "Clean all cache in temp (include other project cache)"
 
     def execute(self, context):
-        container_objs = get_container_objs_from_selection()
-
-        if len(container_objs) == 0:
-            self.report({"WARNING"}, "Cannot find any bioxel container.")
-            return {'FINISHED'}
-
-        fails = []
-        for container_obj in container_objs:
-            for layer_obj in get_container_layer_objs(container_obj):
-                try:
-                    save_layer_cache(layer_obj, self.cache_dir)
-                except:
-                    fails.append(layer_obj)
-
-        if len(fails) == 0:
-            self.report({"INFO"}, f"Successfully saved bioxel layers.")
-        else:
-            self.report(
-                {"WARNING"}, f"{','.join([layer.name for layer in fails])} fail to save.")
-
-        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        context.window_manager.invoke_props_dialog(self,
-                                                   width=500)
-        return {'RUNNING_MODAL'}
-
-
-class CleanAllCaches(bpy.types.Operator):
-    bl_idname = "bioxelnodes.clear_all_caches"
-    bl_label = "Clean All Caches in Temp"
-    bl_description = "Clean all caches saved in temp"
-
-    def execute(self, context):
-        cache_dir = get_cache_dir(context)
+        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 Presets"
+    bl_description = "Render setting presets for bioxel"
+    bl_options = {'UNDO'}
+
+    PRESETS = {
+        "preview_e": "Preview (EEVEE)",
+        "preview_c": "Preview (Cycles)",
+        "production_e": "Production (EEVEE)",
+        "production_c": "Production (Cycles)"
+    }
+
+    preset: bpy.props.EnumProperty(name="Preset",
+                                   default="preview_c",
+                                   items=[(k, v, "")
+                                          for k, v in PRESETS.items()])  # type: ignore
+
+    def execute(self, context):
+        if self.preset == "preview_e":
+            bpy.context.scene.render.engine = 'BLENDER_EEVEE_NEXT'
+            bpy.context.scene.eevee.use_taa_reprojection = False
+            bpy.context.scene.eevee.taa_samples = 16
+            bpy.context.scene.eevee.volumetric_tile_size = '2'
+            bpy.context.scene.eevee.volumetric_shadow_samples = 128
+            bpy.context.scene.eevee.volumetric_samples = 128
+            bpy.context.scene.eevee.volumetric_ray_depth = 16
+            bpy.context.scene.eevee.use_volumetric_shadows = True
+
+        elif self.preset == "production_e":
+            bpy.context.scene.render.engine = 'BLENDER_EEVEE_NEXT'
+            bpy.context.scene.eevee.use_taa_reprojection = False
+            bpy.context.scene.eevee.taa_samples = 16
+            bpy.context.scene.eevee.volumetric_tile_size = '1'
+            bpy.context.scene.eevee.volumetric_shadow_samples = 128
+            bpy.context.scene.eevee.volumetric_samples = 256
+            bpy.context.scene.eevee.volumetric_ray_depth = 16
+            bpy.context.scene.eevee.use_volumetric_shadows = True
+
+        elif self.preset == "preview_c":
+            bpy.context.scene.render.engine = 'CYCLES'
+            bpy.context.scene.cycles.shading_system = True
+            bpy.context.scene.cycles.volume_bounces = 12
+            bpy.context.scene.cycles.transparent_max_bounces = 16
+            bpy.context.scene.cycles.volume_preview_step_rate = 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 = 0.5
+            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 = "A preview scene setting for viewing slicers"
+    bl_icon = "FILE_VOLUME"
+
+    def execute(self, context):
+        bpy.context.scene.eevee.use_taa_reprojection = False
+        bpy.context.scene.eevee.taa_samples = 4
+        bpy.context.scene.eevee.volumetric_tile_size = '2'
+        bpy.context.scene.eevee.volumetric_shadow_samples = 128
+        bpy.context.scene.eevee.volumetric_samples = 128
+        bpy.context.scene.eevee.volumetric_ray_depth = 1
+        bpy.context.scene.eevee.use_volumetric_shadows = False
+
+        for area in bpy.context.screen.areas:
+            if area.type == 'VIEW_3D':
+                area.spaces[0].shading.type = 'MATERIAL'
+                area.spaces[0].shading.studio_light = 'studio.exr'
+                area.spaces[0].shading.studiolight_intensity = 2.5
+                area.spaces[0].shading.use_scene_lights = False
+                area.spaces[0].shading.use_scene_world = False
+
+        return {'FINISHED'}
+
+
+def get_all_layers(layer_filter=None):
+    def _layer_filter(layer_obj):
+        return True
+
+    layer_filter = layer_filter or _layer_filter
+    layer_objs = get_all_layer_objs()
+    return [obj for obj in layer_objs if layer_filter(obj)]
+
+
+class SaveAllLayersCache(bpy.types.Operator, SaveLayersCache):
+    bl_idname = "bioxelnodes.save_all_layers_cache"
+    bl_label = "Save All Layers Cache"
+    bl_description = "Save all cache of this file"
+    bl_icon = "FILE_TICK"
+
+    success_msg = "Successfully saved all layers."
+
+    def get_layers(self, context):
+        def is_not_missing(layer_obj):
+            return not is_missing_layer(layer_obj)
+        return get_all_layers(is_not_missing)
+
+
+class RemoveAllMissingLayers(bpy.types.Operator, RemoveLayers):
+    bl_idname = "bioxelnodes.remove_all_missing_layers"
+    bl_label = "Remove All Missing Layers"
+    bl_description = "Remove all current container missing layers"
+    bl_icon = "BRUSH_DATA"
+
+    success_msg = "Successfully removed all missing layers."
+
+    def get_layers(self, context):
+        def is_missing(layer_obj):
+            return is_missing_layer(layer_obj)
+        return get_all_layers(is_missing)
+
+    def invoke(self, context, event):
+        context.window_manager.invoke_confirm(self,
+                                              event,
+                                              message=f"Are you sure to remove all **Missing** layers?")
         return {'RUNNING_MODAL'}

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

bioxelnodes/preferences.py

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

bioxelnodes/props.py

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

bioxelnodes/utils.py

@@ -1,5 +1,6 @@
 from pathlib import Path
 import shutil
+import bpy
 
 
 def copy_to_dir(source_path, dir_path, new_name=None, exist_ok=True):
@@ -30,3 +31,42 @@ def copy_to_dir(source_path, dir_path, new_name=None, exist_ok=True):
 
     if not target_path.exists():
         raise Exception
+
+
+def select_object(target_obj):
+    for obj in bpy.data.objects:
+        obj.select_set(False)
+
+    target_obj.select_set(True)
+    bpy.context.view_layer.objects.active = target_obj
+
+
+def progress_bar(self, context):
+    row = self.layout.row()
+    row.progress(
+        factor=context.window_manager.bioxelnodes_progress_factor,
+        type="BAR",
+        text=context.window_manager.bioxelnodes_progress_text
+    )
+    row.scale_x = 2
+
+
+def progress_update(context, factor, text=""):
+    context.window_manager.bioxelnodes_progress_factor = factor
+    context.window_manager.bioxelnodes_progress_text = text
+
+
+def get_preferences():
+    return bpy.context.preferences.addons[__package__].preferences
+
+
+def get_cache_dir():
+    preferences = get_preferences()
+    cache_path = Path(preferences.cache_dir, 'VDBs')
+    cache_path.mkdir(parents=True, exist_ok=True)
+    return str(cache_path)
+
+
+def get_use_link():
+    preferences = get_preferences()
+    return preferences.node_import_method == "LINK"

build.py

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

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "bioxelnodes"
-version = "0.3.3"
+version = "1.0.0"
 description = ""
 authors = ["Ma Nan <icrdr2010@outlook.com>"]
 license = "MIT"