Merge pull request #42 from OmooLab/feature/dev

Feature/dev

.gitignore

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

README.md

@@ -1,4 +1,4 @@
-[中文文档](https://uj6xfhbzp0.feishu.cn/wiki/Qx3VwHuNPimeI8kr6nDcvl1DnHf?from=from_copylink)
+[中文文档](https://uj6xfhbzp0.feishu.cn/wiki/LPKEwjooSivxjskWHlCcQznjnNf?from=from_copylink)
 
 # Bioxel Nodes
 
@@ -26,18 +26,18 @@ Welcome to our [discord server](https://discord.gg/pYkNyq2TjE), if you have any
 
 ## Support Multiple Formats
 
-| Format | EXT                                      | Test    |
-| ------ | ---------------------------------------- | ------- |
-| DICOM  | .dcm, .DCM, .DICOM, .ima, .IMA           | ✅ pass |
-| BMP    | .bmp, .BMP                               | ✅ pass |
-| JPEG   | .jpg, .JPG, .jpeg, .JPEG                 | ✅ pass |
-| PNG    | .png, .PNG                               | ✅ pass |
-| TIFF   | .tif, .TIF, .tiff, .TIFF                 | ✅ pass |
-| Nifti  | .nia, .nii, .nii.gz, .hdr, .img, .img.gz | ✅ pass |
-| Nrrd   | .nrrd, .nhdr                             | ✅ pass |
-| HDF5   | .hdf, .h4, .hdf4, .he2, .h5, .hdf5, .he5 | ✅ pass |
-| OME    | .ome.tiff, .ome.tif                      | ✅ pass |
-| MRC    | .mrc, .mrc.gz, .map, .map.gz             | ✅ pass |
+| Format | EXT                                      |
+| ------ | ---------------------------------------- |
+| DICOM  | .dcm, .DCM, .DICOM, .ima, .IMA           |
+| BMP    | .bmp, .BMP                               |
+| JPEG   | .jpg, .JPG, .jpeg, .JPEG                 |
+| PNG    | .png, .PNG                               |
+| TIFF   | .tif, .TIF, .tiff, .TIFF                 |
+| Nifti  | .nia, .nii, .nii.gz, .hdr, .img, .img.gz |
+| Nrrd   | .nrrd, .nhdr                             |
+| HDF5   | .hdf, .h4, .hdf4, .he2, .h5, .hdf5, .he5 |
+| OME    | .ome.tiff, .ome.tif                      |
+| MRC    | .mrc, .mrc.gz, .map, .map.gz             |
 
 ## Support 4D volumetric data
 
@@ -59,16 +59,6 @@ Welcome to our [discord server](https://discord.gg/pYkNyq2TjE), if you have any
 -   Only works with Cycles CPU , Cycles GPU (OptiX), EEVEE
 -   Section surface cannot be generated when convert to mesh (will be supported soon)
 
-## Compatible to Newer Version
-
-**v0.3.x is not compatible to v0.2.x, Updating this addon may break old files. Read the following carefully before upgradation**
-
-Before upgradation, you need to ask yourself whether this project file will be modified again or not, if it's an archived project file, I would recommend that you run **Bioxel Nodes > Save Staged Data** to make the addon nodes permanent. In this way, there will be no potential problem with the nodes not functioning due to the addon update.
-
-After the addon update, your old project files may not work either, this may be because you had executed **Save Staged Data**. If so, you need to execute **Bioxel Nodes > Relink Nodes to Addon** to relink them to make sure that the addon's new functionality and the addon nodes are synchronized.
-
-Also, the older shaders are not based on OSL, so if you find that you can't render volumes, you need to turn on **Open Shading Language (OSL)** in the Render Settings.
-
 ## Roadmap
 
 -   Better multi-format import experience

bioxelnodes/__init__.py

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

bioxelnodes/bioxel/layer.py

@@ -2,12 +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 +1,260 @@
+from ast import literal_eval
+from pathlib import Path
+import bpy
+
+from ..constants import NODE_LIB_DIRPATH, VERSIONS
+from ..utils import get_cache_dir
+
+
+def move_node_to_node(node, target_node, offset=(0, 0)):
+    node.location.x = target_node.location.x + offset[0]
+    node.location.y = target_node.location.y + offset[1]
+
+
+def move_node_between_nodes(node, target_nodes, offset=(0, 0)):
+    xs = []
+    ys = []
+    for target_node in target_nodes:
+        xs.append(target_node.location.x)
+        ys.append(target_node.location.y)
+
+    node.location.x = sum(xs) / len(xs) + offset[0]
+    node.location.y = sum(ys) / len(ys) + offset[1]
+
+
+def get_node_type(node):
+    node_type = type(node).__name__
+    if node_type == "GeometryNodeGroup":
+        node_type = node.node_tree.name
+
+    return node_type
+
+
+def get_nodes_by_type(node_group, type_name: str):
+    return [node for node in node_group.nodes if get_node_type(node) == type_name]
+
+
+def get_container_objs_from_selection():
+    container_objs = []
+    for obj in bpy.context.selected_objects:
+        if get_container_obj(obj):
+            container_objs.append(obj)
+
+    return list(set(container_objs))
+
+
+def get_container_obj(current_obj):
+    if current_obj:
+        if current_obj.get('bioxel_container'):
+            return current_obj
+        elif current_obj.get('bioxel_layer'):
+            parent = current_obj.parent
+            return parent if parent.get('bioxel_container') else None
+    return None
+
+
+def get_layer_prop_value(layer_obj: bpy.types.Object, prop_name: str):
+    node_group = layer_obj.modifiers[0].node_group
+    layer_node = get_nodes_by_type(node_group, "BioxelNodes__Layer")[0]
+    prop = layer_node.inputs.get(prop_name)
+    if prop is None:
+        return None
+
+    value = prop.default_value
+
+    if type(value).__name__ == "bpy_prop_array":
+        value = tuple(value)
+        return tuple([int(v) for v in value]) \
+            if prop in ["shape"] else value
+    elif type(value).__name__ == "str":
+        return str(value)
+    elif type(value).__name__ == "float":
+        value = float(value)
+        return round(value, 2) \
+            if prop in ["bioxel_size"] else value
+    elif type(value).__name__ == "int":
+        value = int(value)
+        return value
+    else:
+        return value
+
+
+def get_layer_name(layer_obj):
+    return get_layer_prop_value(layer_obj, "name")
+
+
+def get_layer_kind(layer_obj):
+    return get_layer_prop_value(layer_obj, "kind")
+
+
+def get_layer_label(layer_obj):
+    name = get_layer_name(layer_obj)
+    # kind = get_layer_kind(layer_obj)
+
+    label = f"{name}"
+
+    if is_missing_layer(layer_obj):
+        return "**MISSING**" + label
+    elif is_temp_layer(layer_obj):
+        return "* " + label
+    else:
+        return label
+
+
+def is_missing_layer(layer_obj):
+    cache_filepath = Path(bpy.path.abspath(
+        layer_obj.data.filepath)).resolve()
+    return not cache_filepath.is_file()
+
+
+def is_temp_layer(layer_obj):
+    cache_filepath = Path(bpy.path.abspath(
+        layer_obj.data.filepath)).resolve()
+    cache_dirpath = Path(get_cache_dir())
+    return cache_dirpath in cache_filepath.parents
+
+
+def set_layer_prop_value(layer_obj: bpy.types.Object, prop: str, value):
+    node_group = layer_obj.modifiers[0].node_group
+    layer_node = get_nodes_by_type(node_group, "BioxelNodes__Layer")[0]
+    layer_node.inputs[prop].default_value = value
+
+
+def get_layer_obj(current_obj: bpy.types.Object):
+    if current_obj:
+        if current_obj.get('bioxel_layer') and current_obj.parent:
+            if current_obj.parent.get('bioxel_container'):
+                return current_obj
+    return None
+
+
+def get_container_layer_objs(container_obj: bpy.types.Object):
+    layer_objs = []
+    for obj in bpy.data.objects:
+        if obj.parent == container_obj and get_layer_obj(obj):
+            layer_objs.append(obj)
+
+    return layer_objs
+
+
+def get_all_layer_objs():
+    layer_objs = []
+    for obj in bpy.data.objects:
+        if get_layer_obj(obj):
+            layer_objs.append(obj)
+
+    return layer_objs
+
+
+def add_driver(target, target_prop, var_sources, expression):
+    driver = target.driver_add(target_prop)
+    is_vector = isinstance(driver, list)
+    drivers = driver if is_vector else [driver]
+
+    for i, driver in enumerate(drivers):
+        for j, var_source in enumerate(var_sources):
+
+            source = var_source['source']
+            prop = var_source['prop']
+
+            var = driver.driver.variables.new()
+            var.name = f"var{j}"
+
+            var.targets[0].id_type = source.id_type
+            var.targets[0].id = source
+            var.targets[0].data_path = f'["{prop}"][{i}]'\
+                if is_vector else f'["{prop}"]'
+
+        driver.driver.expression = expression
+
+
+def add_direct_driver(target, target_prop, source, source_prop):
+    drivers = [
+        {
+            "source": source,
+            "prop": source_prop
+        }
+    ]
+    expression = "var0"
+    add_driver(target, target_prop, drivers, expression)
+
+
+def read_file_prop(content: str):
+    props = {}
+    for line in content.split("\n"):
+        line = line.replace(" ", "")
+        p = line.split("=")[0]
+        if p != "":
+            v = line.split("=")[-1]
+            props[p] = v
+    return props
+
+
+def write_file_prop(props: dict):
+    lines = []
+    for p, v in props.items():
+        lines.append(f"{p} = {v}")
+    return "\n".join(lines)
+
+
+def set_file_prop(prop, value):
+    if bpy.data.texts.get("BioxelNodes") is None:
+        bpy.data.texts.new("BioxelNodes")
+
+    props = read_file_prop(bpy.data.texts["BioxelNodes"].as_string())
+    props[prop] = value
+    bpy.data.texts["BioxelNodes"].clear()
+    bpy.data.texts["BioxelNodes"].write(write_file_prop(props))
+
+
+def get_file_prop(prop):
+    if bpy.data.texts.get("BioxelNodes") is None:
+        bpy.data.texts.new("BioxelNodes")
+
+    props = read_file_prop(bpy.data.texts["BioxelNodes"].as_string())
+    return props.get(prop)
+
+
+def get_node_version():
+    node_version = get_file_prop("node_version")
+    return literal_eval(node_version) if node_version else None
+
+
+def is_incompatible():
+    node_version = get_node_version()
+    if node_version is None:
+        for node_group in bpy.data.node_groups:
+            if node_group.name.startswith("BioxelNodes"):
+                return True
+    else:
+        addon_version = VERSIONS[0]["node_version"]
+        if node_version[0] != addon_version[0]\
+                or node_version[1] != addon_version[1]:
+            return True
+
+    return False
+
+
+def get_node_lib_path(node_version):
+    version_str = "v"+".".join([str(i) for i in list(node_version)])
+    lib_filename = f"BioxelNodes_{version_str}.blend"
+    return Path(NODE_LIB_DIRPATH,
+                lib_filename).resolve()
+
+
+def local_lib_not_updated():
+    addon_version = VERSIONS[0]["node_version"]
+    addon_lib_path = get_node_lib_path(addon_version)
+
+    use_local = False
+    for node_group in bpy.data.node_groups:
+        if node_group.name.startswith("BioxelNodes"):
+            lib = node_group.library
+            if lib:
+                lib_path = Path(bpy.path.abspath(lib.filepath)).resolve()
+                if lib_path != addon_lib_path:
+                    use_local = True
+                    break
+
+    not_update = get_node_version() != addon_version
+    return use_local and not_update

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,
+                                       use_link=get_use_link())
+        fetch_node.label = get_layer_prop_value(layer_obj, "name")
+        fetch_node.inputs[0].default_value = layer_obj
+
+        if len(output_node.inputs[0].links) == 0:
+            node_group.links.new(fetch_node.outputs[0],
+                                 output_node.inputs[0])
+            move_node_to_node(fetch_node, output_node, (-600, 0))
+        else:
+            move_node_to_node(fetch_node, output_node, (0, -100 * (i+1)))
+
+    return container_obj
+
+
 def container_to_obj(container: Container,
                      scene_scale: float,
+                     step_size: float,
                      cache_dir: str):
     # Wrapper a Container
 
@@ -151,30 +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 +144,37 @@ def layer_to_obj(layer: Layer,
         vdb.write(str(cache_filepath), grids=[grid])
         cache_filepaths = [cache_filepath]
 
-        print(f"Loading the Cache of {layer.name}...")
-        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,
+                                   use_link=get_use_link())
 
     layer_node.inputs['name'].default_value = layer.name
     layer_node.inputs['shape'].default_value = layer.shape
@@ -207,19 +185,18 @@ def layer_to_obj(layer: Layer,
             affine_key = f"affine{i}{j}"
             layer_node.inputs[affine_key].default_value = layer.affine[j, i]
 
-    layer_node.inputs['id'].default_value = random.randint(-200000000,
-                                                              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 +206,6 @@ def layer_to_obj(layer: Layer,
     move_node_between_nodes(
         layer_node, [input_node, output_node])
 
+    layer_obj.parent = container_obj
+
     return layer_obj

bioxelnodes/bioxelutils/node.py

@@ -1,26 +1,70 @@
-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 bpy
+
+from .common import get_file_prop, get_node_lib_path, set_file_prop
+from ..exceptions import Incompatible, NoFound
+
+from ..constants import VERSIONS
 
 
-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]
+    # added node is always from latest node version
+    addon_version = VERSIONS[0]["node_version"]
+    addon_lib_path = get_node_lib_path(addon_version)
+
+    if get_file_prop("node_version") is None:
+        set_file_prop("node_version", addon_version)
+
+    local_lib_path = None
+    for node_group in bpy.data.node_groups:
+        if node_group.name.startswith("BioxelNodes"):
+            lib = node_group.library
+            if lib:
+                lib_path = Path(bpy.path.abspath(lib.filepath)).resolve()
+                if lib_path != addon_lib_path:
+                    local_lib_path = lib_path
+                    break
+
+    # local lib first
+    lib_path = local_lib_path or addon_lib_path
+    bpy.ops.wm.append('EXEC_DEFAULT',
+                      directory=f"{lib_path.as_posix()}/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, node_label=None, use_link=True):
+    node_type = f"BioxelNodes_{node_name}"
+    node_label = node_label or node_name
+
+    # Deselect all nodes first
+    for node in node_group.nodes:
+        if node.select:
+            node.select = False
+
+    get_node_group(node_type, use_link)
+    node = node_group.nodes.new("GeometryNodeGroup")
+    assign_node_group(node, node_type)
+
+    node.label = node_label
+    node.show_options = False
+    return node

bioxelnodes/blender_manifest.toml

@@ -1,7 +1,7 @@
 schema_version = "1.0.0"
 
 id = "bioxelnodes"
-version = "0.3.3"
+version = "1.0.0"
 name = "Bioxel Nodes"
 tagline = "For scientific volumetric data visualization in Blender"
 maintainer = "Ma Nan <icrdr2010@outlook.com>"
@@ -19,10 +19,10 @@ wheels = [
   "./wheels/SimpleITK-2.3.1-cp311-cp311-macosx_10_9_x86_64.whl",
   "./wheels/SimpleITK-2.3.1-cp311-cp311-macosx_11_0_arm64.whl",
   "./wheels/SimpleITK-2.3.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
-  "./wheels/lxml-5.2.2-cp311-cp311-win_amd64.whl",
-  "./wheels/lxml-5.2.2-cp311-cp311-macosx_10_9_arm64.whl",
-  "./wheels/lxml-5.2.2-cp311-cp311-macosx_10_9_x86_64.whl",
-  "./wheels/lxml-5.2.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
+  "./wheels/lxml-5.3.0-cp311-cp311-win_amd64.whl",
+  "./wheels/lxml-5.3.0-cp311-cp311-macosx_10_9_arm64.whl",
+  "./wheels/lxml-5.3.0-cp311-cp311-macosx_10_9_x86_64.whl",
+  "./wheels/lxml-5.3.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
   "./wheels/h5py-3.11.0-cp311-cp311-win_amd64.whl",
   "./wheels/h5py-3.11.0-cp311-cp311-macosx_11_0_arm64.whl",
   "./wheels/h5py-3.11.0-cp311-cp311-macosx_10_9_x86_64.whl",
@@ -30,9 +30,8 @@ wheels = [
   "./wheels/tifffile-2024.7.24-py3-none-any.whl",
   "./wheels/pyometiff-1.0.0-py3-none-any.whl",
   "./wheels/mrcfile-1.5.1-py2.py3-none-any.whl",
-  "./wheels/transforms3d-0.4.2-py3-none-any.whl",
+  "./wheels/transforms3d-0.4.2-py3-none-any.whl"
 ]
 
 [permissions]
 files = "Import/export volume data from/to disk"
-

bioxelnodes/constants.py

@@ -0,0 +1,226 @@
+from pathlib import Path
+
+VERSIONS = [{"label": "Current", "node_version": (1, 0, 0)},
+            {"label": "v0.3.x", "node_version": (0, 3, 3)},
+            {"label": "v0.2.x", "node_version": (0, 2, 9)}]
+
+NODE_LIB_DIRPATH = Path(Path(__file__).parent,
+                        "assets/Nodes").resolve()
+
+MENU_ITEMS = [
+    {
+        'label': 'Component',
+        'icon': 'OUTLINER_DATA_VOLUME',
+        'items': [
+            {
+                'label': 'Cutout by Threshold',
+                'icon': 'EMPTY_SINGLE_ARROW',
+                'name': 'CutoutByThreshold',
+                'description': ''
+            },
+            {
+                'label': 'Cutout by Range',
+                'icon': 'IPO_CONSTANT',
+                'name': 'CutoutByRange',
+                'description': ''
+            },
+            {
+                'label': 'Cutout by Hue',
+                'icon': 'COLOR',
+                'name': 'CutoutByHue',
+                'description': ''
+            },
+            "separator",
+            {
+                'label': 'To Surface',
+                'icon': 'MESH_DATA',
+                'name': 'ToSurface',
+                'description': ''
+            },
+            {
+                'label': 'Join Component',
+                'icon': 'CONSTRAINT_BONE',
+                'name': 'JoinComponent',
+                'description': ''
+            },
+            {
+                'label': 'Slice',
+                'icon': 'TEXTURE',
+                'name': 'Slice',
+                'description': ''
+            }
+        ]
+    },
+    {
+        'label': 'Property',
+        'icon': 'PROPERTIES',
+        'items': [
+            {
+                'label': 'Set Properties',
+                'icon': 'PROPERTIES',
+                'name': 'SetProperties',
+                'description': ''
+            },
+            "separator",
+            {
+                'label': 'Set Color',
+                'icon': 'IPO_SINE',
+                'name': 'SetColor',
+                'description': ''
+            },
+            {
+                'label': 'Set Color by Color',
+                'icon': 'IPO_QUINT',
+                'name': 'SetColorByColor',
+                'description': ''
+            },
+            {
+                'label': 'Set Color by Ramp 2',
+                'icon': 'IPO_QUAD',
+                'name': 'SetColorByRamp2',
+                'description': ''
+            },
+            {
+                'label': 'Set Color by Ramp 3',
+                'icon': 'IPO_CUBIC',
+                'name': 'SetColorByRamp3',
+                'description': ''
+            },
+            {
+                'label': 'Set Color by Ramp 4',
+                'icon': 'IPO_QUART',
+                'name': 'SetColorByRamp4',
+                'description': ''
+            },
+            {
+                'label': 'Set Color by Ramp 5',
+                'icon': 'IPO_QUINT',
+                'name': 'SetColorByRamp5',
+                'description': ''
+            }
+        ]
+    },
+    {
+        'label': 'Surface',
+        'icon': 'MESH_DATA',
+        'items': [
+            {
+                'label': 'Membrane Shader',
+                'icon': 'NODE_MATERIAL',
+                'name': 'AssignMembraneShader',
+                'description': ''
+            },
+            {
+                'label': 'Solid Shader',
+                'icon': 'SHADING_SOLID',
+                'name': 'AssignSolidShader',
+                'description': ''
+            },
+            {
+                'label': 'Slime Shader',
+                'icon': 'OUTLINER_DATA_META',
+                'name': 'AssignSlimeShader',
+                'description': ''
+            },
+
+        ]
+    },
+    {
+        'label': 'Transform',
+        'icon': 'EMPTY_AXIS',
+        'items': [
+            {
+                'label': 'Transform',
+                'icon': 'EMPTY_AXIS',
+                'name': 'Transform',
+                'description': ''
+            },
+            {
+                'label': 'Transform Parent',
+                'icon': 'ORIENTATION_PARENT',
+                'name': 'TransformParent',
+                'description': ''
+            },
+            {
+                'label': 'ReCenter',
+                'icon': 'PROP_CON',
+                'name': 'ReCenter',
+                'description': ''
+            }
+        ]
+    },
+    {
+        'label': 'Cut',
+        'icon': 'MOD_BEVEL',
+        'items': [
+            {
+                'label': 'Cut',
+                'icon': 'MOD_BEVEL',
+                'name': 'Cut',
+                'description': ''
+            },
+            "separator",
+            {
+                'label': 'Primitive Cutter',
+                'icon': 'MOD_LINEART',
+                'name': 'PrimitiveCutter',
+                'description': ''
+            },
+            {
+                'label': 'Object Cutter',
+                'icon': 'MESH_PLANE',
+                'name': 'ObjectCutter',
+                'description': ''
+            }
+        ]
+    },
+    {
+        'label': 'Extra',
+        'icon': 'MODIFIER',
+        'items': [
+            {
+                'label': 'Fetch Surface',
+                'icon': 'OUTLINER_OB_MESH',
+                'name': 'FetchSurface',
+                'description': ''
+            },
+            {
+                'label': 'Fetch Volume',
+                'icon': 'OUTLINER_OB_VOLUME',
+                'name': 'FetchVolume',
+                'description': ''
+            },
+            {
+                'label': 'Fetch Shape Wire',
+                'icon': 'FILE_VOLUME',
+                'name': 'FetchShapeWire',
+                'description': ''
+            },
+            {
+                'label': 'Fetch Bbox Wire',
+                'icon': 'MESH_CUBE',
+                'name': 'FetchBboxWire',
+                'description': ''
+            },
+            "separator",
+            {
+                'label': 'Inflate',
+                'icon': 'OUTLINER_OB_META',
+                'name': 'Inflate',
+                'description': ''
+            },
+            {
+                'label': 'Smooth',
+                'icon': 'MOD_SMOOTH',
+                'name': 'Smooth',
+                'description': ''
+            },
+            {
+                'label': 'Remove Small Island',
+                'icon': 'FORCE_LENNARDJONES',
+                'name': 'RemoveSmallIsland',
+                'description': ''
+            }
+        ]
+    }
+]

bioxelnodes/customnodes/__init__.py

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

bioxelnodes/customnodes/menus.py

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

bioxelnodes/customnodes/nodes.py

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

bioxelnodes/exceptions.py

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

bioxelnodes/menus.py

@@ -1,156 +1,186 @@
 import bpy
 
-from .bioxelutils.container import get_container_objs_from_selection
-from .operators.layer import (CombineLabels, SignScalar,
+from .constants import MENU_ITEMS, VERSIONS
+from .node_menu import NodeMenu
+
+from .bioxelutils.common import (get_container_obj,
+                                 get_container_layer_objs, get_layer_label,
+                                 get_layer_prop_value, get_node_version, is_incompatible)
+from .operators.layer import (FetchLayer, RelocateLayer, RetimeLayer, RenameLayer,
+                              RemoveSelectedLayers, SaveSelectedLayersCache,
+                              ResampleLayer, SignScalar, CombineLabels,
                               FillByLabel, FillByThreshold, FillByRange)
-from .operators.container import (SaveContainer, LoadContainer,
+from .operators.container import (AddLocator, AddSlicer, 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 IncompatibleMenu(bpy.types.Menu):
+    bl_idname = "BIOXELNODES_MT_INCOMPATIBLE"
+    bl_label = "Bioxel Nodes"
+
+    def draw(self, context):
+        tip_text = "please downgrade addon version."
+        node_version = get_node_version()
+        if node_version:
+            version_str = "v"+".".join([str(i) for i in list(node_version)])
+            tip_text = f"please downgrade addon version to {version_str}."
+
+        layout = self.layout
+        layout.label(text="Incompatible node version detected.")
+        layout.separator()
+        layout.label(
+            text="If you still want to edit this file with bioxel nodes, ")
+        layout.label(text=tip_text)
+        layout.separator()
+        layout.label(text="If this file is archived, "
+                     "please relink node library, ")
+        layout.label(text="check if it still works, "
+                     "then save node library.")
+        layout.separator()
+        layout.menu(ReLinkNodeLibMenu.bl_idname)
+        layout.operator(SaveNodeLib.bl_idname)
+
+        layout.separator()
+        layout.menu(DangerZoneMenu.bl_idname)
+
+        layout.separator()
+        layout.menu(RenderSettingMenu.bl_idname)
 
 
-class PickFromContainerMenu(bpy.types.Menu):
+class FetchLayerMenu(bpy.types.Menu):
+    bl_idname = "BIOXELNODES_MT_ADD_LAYER"
+    bl_label = "Fetch Layer"
+
+    def draw(self, context):
+        container_obj = get_container_obj(bpy.context.active_object)
+        layer_objs = get_container_layer_objs(container_obj)
+        layout = self.layout
+
+        for layer_obj in layer_objs:
+            op = layout.operator(FetchLayer.bl_idname,
+                                 text=get_layer_label(layer_obj))
+            op.layer_obj_name = layer_obj.name
+
+
+class ExtractFromContainerMenu(bpy.types.Menu):
     bl_idname = "BIOXELNODES_MT_PICK"
-    bl_label = "Pick from Container"
+    bl_label = "Extract from Container"
 
     def draw(self, context):
         layout = self.layout
-        layout.operator(PickMesh.bl_idname)
-        layout.operator(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.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)
+        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)
 
 
-def TOPBAR_FILE_IMPORT(self, context):
-    layout = self.layout
-    is_selected = container_is_selected()
+class ReLinkNodeLibMenu(bpy.types.Menu):
+    bl_idname = "BIOXELNODES_MT_RELINK"
+    bl_label = "Relink Node Library"
 
-    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 index, version in enumerate(VERSIONS):
+            op = layout.operator(ReLinkNodeLib.bl_idname,
+                                 text=version["label"])
+            op.index = index
 
 
-def TOPBAR_FILE_EXPORT(self, context):
-    layout = self.layout
-    layout.separator()
-    layout.operator(ExportVolumetricData.bl_idname,
-                    text="Bioxel Layer (.vdb)")
+class RenderSettingMenu(bpy.types.Menu):
+    bl_idname = "BIOXELNODES_MT_RENDER"
+    bl_label = "Render Setting Presets"
+
+    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 VIEW3D_OBJECT(self, context):
-    layout = self.layout
-    layout.separator()
-    layout.menu(BioxelNodesView3DMenu.bl_idname, icon="FILE_VOLUME")
+class DangerZoneMenu(bpy.types.Menu):
+    bl_idname = "BIOXELNODES_MT_DANGER"
+    bl_label = "Danger Zone"
 
-
-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):
@@ -159,39 +189,231 @@ 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):
     layout = self.layout
-    layout.menu(BioxelNodesTopbarMenu.bl_idname)
+
+    if is_incompatible():
+        layout.menu(IncompatibleMenu.bl_idname)
+    else:
+        layout.menu(BioxelNodesTopbarMenu.bl_idname)
+
+
+class NodeHeadMenu(bpy.types.Menu):
+    bl_idname = "BIOXELNODES_MT_NODE_HEAD"
+    bl_label = "Bioxel Nodes"
+    bl_icon = "FILE_VOLUME"
+
+    def draw(self, context):
+
+        layout = self.layout
+        layout.menu(AddLayerMenu.bl_idname,
+                    icon=AddLayerMenu.bl_icon)
+        layout.operator(SaveContainer.bl_idname)
+
+        layout.separator()
+        layout.operator(ContainerProps.bl_idname)
+        layout.menu(ExtractFromContainerMenu.bl_idname)
+
+        layout.separator()
+        layout.operator(SaveContainerLayersCache.bl_idname,
+                        icon=SaveContainerLayersCache.bl_icon)
+        layout.operator(RemoveContainerMissingLayers.bl_idname)
+
+        layout.separator()
+        layout.operator(AddLocator.bl_idname,
+                        icon=AddLocator.bl_icon)
+        layout.operator(AddSlicer.bl_idname,
+                        icon=AddSlicer.bl_icon)
+        layout.menu(AddCutterMenu.bl_idname)
+
+        layout.separator()
+        layout.menu(FetchLayerMenu.bl_idname)
+
+
+class NodeContextMenu(bpy.types.Menu):
+    bl_idname = "BIOXELNODES_MT_NODE_CONTEXT"
+    bl_label = "Bioxel Nodes"
+    bl_icon = "FILE_VOLUME"
+
+    def draw(self, context):
+        layout = self.layout
+        layout.operator(SaveSelectedLayersCache.bl_idname,
+                        icon=SaveSelectedLayersCache.bl_icon)
+        layout.operator(RemoveSelectedLayers.bl_idname)
+
+        layout.separator()
+        layout.operator(RenameLayer.bl_idname,
+                        icon=RenameLayer.bl_icon)
+        layout.operator(RetimeLayer.bl_idname)
+        layout.operator(RelocateLayer.bl_idname)
+
+        layout.separator()
+        layout.operator(ResampleLayer.bl_idname,
+                        icon=ResampleLayer.bl_icon)
+        layout.operator(SignScalar.bl_idname)
+        layout.operator(FillByThreshold.bl_idname)
+        layout.operator(FillByRange.bl_idname)
+        layout.operator(FillByLabel.bl_idname)
+        layout.operator(CombineLabels.bl_idname)
+
+
+def NODE_CONTEXT(self, context):
+    if is_incompatible():
+        return
+
+    container_obj = context.object
+    is_geo_nodes = context.area.ui_type == "GeometryNodeTree"
+    is_container = get_container_obj(container_obj)
+
+    if not is_geo_nodes or not is_container:
+        return
+
+    layout = self.layout
+    layout.separator()
+    layout.menu(NodeContextMenu.bl_idname)
+
+
+def NODE_HEAD(self, context):
+    if is_incompatible():
+        return
+
+    container_obj = context.object
+    is_geo_nodes = context.area.ui_type == "GeometryNodeTree"
+    is_container = get_container_obj(container_obj)
+
+    if not is_geo_nodes or not is_container:
+        return
+
+    layout = self.layout
+    layout.separator()
+    layout.menu(NodeHeadMenu.bl_idname)
+
+
+def NODE_PROP(self, context):
+    if is_incompatible():
+        return
+
+    container_obj = context.object
+    is_geo_nodes = context.area.ui_type == "GeometryNodeTree"
+    is_container = get_container_obj(container_obj)
+    self.bl_label = "Group"
+
+    if not is_geo_nodes or not is_container:
+        return
+
+    if container_obj.modifiers[0].node_group != context.space_data.edit_tree:
+        return
+
+    self.bl_label = "Bioxel Nodes"
+
+    layer_list_UL = bpy.context.window_manager.bioxelnodes_layer_list_UL
+    layer_list = layer_list_UL.layer_list
+    layer_list.clear()
+
+    for layer_obj in get_container_layer_objs(container_obj):
+        layer_item = layer_list.add()
+        layer_item.label = get_layer_label(layer_obj)
+        layer_item.obj_name = layer_obj.name
+        layer_item.info_text = "\n".join([f"{prop}: {get_layer_prop_value(layer_obj, prop)}"
+                                          for prop in ["kind",
+                                                       "bioxel_size",
+                                                       "shape",
+                                                       "frame_count",
+                                                       "channel_count",
+                                                       "min", "max"]])
+
+    layout = self.layout
+    layout.label(text="Layer List")
+    split = layout.row()
+    split.template_list(listtype_name="BIOXELNODES_UL_layer_list",
+                        list_id="layer_list",
+                        dataptr=layer_list_UL,
+                        propname="layer_list",
+                        active_dataptr=layer_list_UL,
+                        active_propname="layer_list_active",
+                        item_dyntip_propname="info_text",
+                        rows=20)
+
+    # sidebar = split.column(align=True)
+    # sidebar.menu(AddLayerMenu.bl_idname,
+    #              icon=AddLayerMenu.bl_icon, text="")
+
+    # sidebar.operator(SaveContainerLayersCache.bl_idname,
+    #                  icon=SaveContainerLayersCache.bl_icon, text="")
+    # sidebar.operator(RemoveContainerMissingLayers.bl_idname,
+    #                  icon=RemoveContainerMissingLayers.bl_icon, text="")
+
+    # sidebar.separator()
+    # sidebar.operator(SaveSelectedLayersCache.bl_idname,
+    #                  icon=SaveSelectedLayersCache.bl_icon, text="")
+    # sidebar.operator(RemoveSelectedLayers.bl_idname,
+    #                  icon=RemoveSelectedLayers.bl_icon, text="")
+
+    # sidebar.separator()
+    # sidebar.operator(RenameLayer.bl_idname,
+    #                  icon=RenameLayer.bl_icon, text="")
+    # sidebar.operator(ResampleLayer.bl_idname,
+    #                  icon=ResampleLayer.bl_icon, text="")
+    # sidebar.operator(RetimeLayer.bl_idname,
+    #                  icon=RetimeLayer.bl_icon, text="")
+
+    # sidebar.separator()
+    # sidebar.operator(SignScalar.bl_idname,
+    #                  icon=SignScalar.bl_icon, text="")
+    # sidebar.operator(FillByThreshold.bl_idname,
+    #                  icon=FillByThreshold.bl_icon, text="")
+    # sidebar.operator(FillByRange.bl_idname,
+    #                  icon=FillByRange.bl_icon, text="")
+    # sidebar.operator(FillByLabel.bl_idname,
+    #                  icon=FillByLabel.bl_icon, text="")
+
+    # sidebar.separator()
+    # layout.separator()
+
+
+def VIEW3D_TOPBAR(self, context):
+    layout = self.layout
+    layout.operator(SliceViewer.bl_idname)
+
+
+node_menu = NodeMenu(
+    menu_items=MENU_ITEMS
+)
 
 
 def add():
-    bpy.types.TOPBAR_MT_file_import.append(TOPBAR_FILE_IMPORT)
-    # 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 +77,34 @@ 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,
+                                            node_label=f"Fetch {self.object_type}",
+                                            use_link=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 +113,78 @@ 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 +208,22 @@ class AddCutter():
 
             # Finish up, write the bmesh back to the mesh
             bm.to_mesh(pie_mesh)
-            bpy.context.view_layer.objects.active = pie
+            # bpy.context.view_layer.objects.active = pie
 
         cutter_obj = bpy.context.active_object
+
+        # vcos = [container_obj.matrix_world @
+        #         v.co for v in container_obj.data.vertices]
+
+        # def find_center(l): return (max(l) + min(l)) / 2
+
+        # x, y, z = [[v[i] for v in vcos] for i in range(3)]
+        # center = [find_center(axis) for axis in [x, y, z]]
+
+        # cutter_obj.location = center
+        name = f"{self.cutter_type.capitalize()}_Cutter"
+        cutter_obj.name = name
+        cutter_obj.data.name = name
         cutter_obj.visible_camera = False
         cutter_obj.visible_diffuse = False
         cutter_obj.visible_glossy = False
@@ -219,17 +232,29 @@ class AddCutter():
         cutter_obj.visible_shadow = False
         cutter_obj.hide_render = True
         cutter_obj.display_type = 'WIRE'
+        cutter_obj.lineart.usage = 'EXCLUDE'
+
+        select_object(container_obj)
 
         modifier = container_obj.modifiers[0]
         node_group = modifier.node_group
-        cutter_node = custom_nodes.add_node(node_group, node_type)
-        cutter_node.inputs[0].default_value = cutter_obj
 
         cut_nodes = get_nodes_by_type(node_group,
                                       'BioxelNodes_Cut')
-        output_node = get_nodes_by_type(node_group, 'NodeGroupOutput')[0]
         if len(cut_nodes) == 0:
-            cut_node = custom_nodes.add_node(node_group, 'BioxelNodes_Cut')
+            cutter_node = add_node_to_graph("ObjectCutter",
+                                            node_group,
+                                            node_label=name,
+                                            use_link=get_use_link())
+            cutter_node.inputs[0].default_value = self.cutter_type.capitalize()
+            cutter_node.inputs[1].default_value = cutter_obj
+
+            cut_node = add_node_to_graph("Cut",
+                                         node_group,
+                                         use_link=get_use_link())
+
+            output_node = get_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 +272,13 @@ 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 +286,243 @@ class AddCutter():
 class AddPlaneCutter(bpy.types.Operator, AddCutter):
     bl_idname = "bioxelnodes.add_plane_cutter"
     bl_label = "Add a Plane Cutter"
-    bl_description = "Add a Plane Cutter to Container"
-    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,
+                                       use_link=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,
+                                        node_label="Transform Parent",
+                                        use_link=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]*10
             container_obj = container_to_obj(container,
                                              scene_scale=self.scene_scale,
-                                             cache_dir=get_cache_dir(context))
+                                             step_size=step_size,
+                                             cache_dir=get_cache_dir())
 
         select_object(container_obj)
 
         # Change render setting for better result
         if is_first_import:
-            change_render_setting(context)
+            bpy.ops.bioxelnodes.render_setting_preset('EXEC_DEFAULT',
+                                                      preset="balance")
+            bpy.context.scene.render.engine = 'CYCLES'
 
         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

@@ -4,20 +4,16 @@ 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.node import add_node_to_graph
+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, move_node_to_node, set_layer_prop_value)
+from ..bioxelutils.layer import layer_to_obj, obj_to_layer
+from ..utils import get_cache_dir, copy_to_dir, get_use_link
 
 
 def get_label_layer_selection(self, context):
@@ -25,86 +21,332 @@ 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):
+        orig_node = context.selected_nodes[0]
+        layer_obj = layer_to_obj(layer,
+                                 container_obj=context.object,
+                                 cache_dir=get_cache_dir())
+        node_group = context.space_data.edit_tree
+        fetch_node = add_node_to_graph("FetchLayer",
+                                       node_group,
+                                       use_link=get_use_link())
+        fetch_node.label = get_layer_prop_value(layer_obj, "name")
+        fetch_node.inputs[0].default_value = layer_obj
+        move_node_to_node(fetch_node, orig_node, (0, -100))
+
+    def execute(self, context):
+        layer_obj = get_selected_layer(context)
+        if layer_obj == None:
+            self.report({"WARNING"}, "Get no layer.")
+            return {'FINISHED'}
+
+        if is_missing_layer(layer_obj):
+            self.report({"WARNING"}, "Selected layer is lost.")
+            return {'FINISHED'}
+
+        orig_layer = obj_to_layer(layer_obj)
+        try:
+            new_layer = self.operate(orig_layer, context)
+        except NoContent as e:
+            self.report({"WARNING"}, e.message)
+            return {'FINISHED'}
+
+        self.add_layer_node(context, new_layer)
         return {'FINISHED'}
 
 
-class FillOperator(ScalarOperator):
+class LayerOperator():
+
+    def operate(self, layer_obj: bpy.types.Object, context):
+        """do the operation"""
+        ...
+
+    def execute(self, context):
+        layer_obj = get_selected_layer(context)
+        if layer_obj == None:
+            self.report({"WARNING"}, "Get no layer.")
+            return {'FINISHED'}
+
+        if is_missing_layer(layer_obj):
+            self.report({"WARNING"}, "Selected layer is lost.")
+            return {'FINISHED'}
+
+        self.operate(layer_obj, context)
+
+        return {'FINISHED'}
+
+
+class RetimeLayer(bpy.types.Operator, LayerOperator):
+    bl_idname = "bioxelnodes.retime_layer"
+    bl_label = "Retime Sequence"
+    bl_description = "Retime layer time sequence"
+    bl_icon = "TIME"
+
+    frame_duration: bpy.props.IntProperty(name="Frames")  # type: ignore
+    frame_start: bpy.props.IntProperty(name="Start")  # type: ignore
+    frame_offset: bpy.props.IntProperty(name="Offset")  # type: ignore
+    sequence_mode: bpy.props.EnumProperty(name="Mode",
+                                          default="REPEAT",
+                                          items=[("CLIP", "Clip", ""),
+                                                 ("EXTEND", "Extend", ""),
+                                                 ("REPEAT", "Repeat", ""),
+                                                 ("PING_PONG", "Ping-Pong", "")])  # type: ignore
+
+    def operate(self, layer_obj, context):
+        layer_obj.data.frame_duration = self.frame_duration
+        layer_obj.data.frame_start = self.frame_start
+        layer_obj.data.frame_offset = self.frame_offset
+        layer_obj.data.sequence_mode = self.sequence_mode
+
     def invoke(self, context, event):
-        self.base_obj = get_layer_obj(bpy.context.active_object)
-        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 +354,52 @@ 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 +413,200 @@ 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 +1,52 @@
-import re
 import bpy
 from pathlib import Path
 import shutil
 
+from ..bioxelutils.common import get_all_layer_objs, get_node_lib_path, get_node_version, is_missing_layer, set_file_prop
+from .layer import RemoveLayers, SaveLayersCache
 
-from ..utils import copy_to_dir
-from .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_DIRPATH, VERSIONS
+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'}
+
+    index: bpy.props.IntProperty()  # 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
+        node_version = VERSIONS[self.index]['node_version']
+        lib_path = get_node_lib_path(node_version)
+
+        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_path)
+            # FIXME: may cause crash
+            node_lib.reload()
+
+        set_file_prop("node_version", node_version)
 
         self.report({"INFO"}, f"Successfully relinked.")
 
         return {'FINISHED'}
 
 
-def save_layer_cache(layer_obj, output_dir):
-    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 +55,200 @@ 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))
+        node_version = get_node_version()
+        if node_version is None:
+            node_version = VERSIONS[0]["node_version"]
+        else:
+            if node_version not in [v["node_version"] for v in VERSIONS]:
+                node_version = VERSIONS[0]["node_version"]
                 
-            for file in files:
-                file_name = Path(file).name
-                # "//"
-                lib_dir = bpy.path.abspath(self.lib_dir)
+        lib_path = get_node_lib_path(node_version)
         
-                output_path: Path = Path(lib_dir, file_name).resolve()
-                source_path: Path = Path(file).resolve()
+        lib_dir = bpy.path.abspath(self.lib_dir)
+        local_lib_path: Path = Path(lib_dir, lib_path.name).resolve()
+        node_lib_path: Path = lib_path
+        blend_path = Path(bpy.path.abspath("//")).resolve()
 
-                if output_path != source_path:
-                    shutil.copy(source_path, output_path)
+        if local_lib_path != node_lib_path:
+            shutil.copy(node_lib_path, local_lib_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))
+        libs = []
+        for node_group in bpy.data.node_groups:
+            if node_group.name.startswith("BioxelNodes"):
+                if node_group.library:
+                    libs.append(node_group.library)
 
-                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.")
+        libs = list(set(libs))
+        for lib in libs:
+            lib.filepath = bpy.path.relpath(str(local_lib_path),
+                                            start=str(blend_path))
 
         return {'FINISHED'}
 
     def invoke(self, context, event):
-        context.window_manager.invoke_props_dialog(self,
-                                                   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 = {
+        "performance": "Performance",
+        "balance": "Balance",
+        "quality": "Quality",
+    }
+
+    preset: bpy.props.EnumProperty(name="Preset",
+                                   default="balance",
+                                   items=[(k, v, "")
+                                          for k, v in PRESETS.items()])  # type: ignore
+
+    def execute(self, context):
+        if self.preset == "performance":
+            # EEVEE
+            bpy.context.scene.eevee.use_taa_reprojection = False
+            bpy.context.scene.eevee.volumetric_tile_size = '2'
+            bpy.context.scene.eevee.volumetric_shadow_samples = 32
+            bpy.context.scene.eevee.volumetric_samples = 64
+            bpy.context.scene.eevee.volumetric_ray_depth = 1
+            bpy.context.scene.eevee.use_volumetric_shadows = True
+
+            # Cycles
+            bpy.context.scene.cycles.shading_system = True
+            bpy.context.scene.cycles.volume_bounces = 0
+            bpy.context.scene.cycles.transparent_max_bounces = 4
+            bpy.context.scene.cycles.volume_preview_step_rate = 4
+            bpy.context.scene.cycles.volume_step_rate = 4
+
+        elif self.preset == "balance":
+            # EEVEE
+            bpy.context.scene.eevee.use_taa_reprojection = False
+            bpy.context.scene.eevee.volumetric_tile_size = '2'
+            bpy.context.scene.eevee.volumetric_shadow_samples = 64
+            bpy.context.scene.eevee.volumetric_samples = 128
+            bpy.context.scene.eevee.volumetric_ray_depth = 8
+            bpy.context.scene.eevee.use_volumetric_shadows = True
+
+            # Cycles
+            bpy.context.scene.cycles.shading_system = True
+            bpy.context.scene.cycles.volume_bounces = 4
+            bpy.context.scene.cycles.transparent_max_bounces = 8
+            bpy.context.scene.cycles.volume_preview_step_rate = 1
+            bpy.context.scene.cycles.volume_step_rate = 1
+
+        elif self.preset == "quality":
+            # EEVEE
+            bpy.context.scene.eevee.use_taa_reprojection = False
+            bpy.context.scene.eevee.volumetric_tile_size = '2'
+            bpy.context.scene.eevee.volumetric_shadow_samples = 128
+            bpy.context.scene.eevee.volumetric_samples = 256
+            bpy.context.scene.eevee.volumetric_ray_depth = 16
+            bpy.context.scene.eevee.use_volumetric_shadows = True
+
+            # Cycles
+            bpy.context.scene.cycles.shading_system = True
+            bpy.context.scene.cycles.volume_bounces = 8
+            bpy.context.scene.cycles.transparent_max_bounces = 16
+            bpy.context.scene.cycles.volume_preview_step_rate = 0.5
+            bpy.context.scene.cycles.volume_step_rate = 0.5
+
+        return {'FINISHED'}
+
+
+class SliceViewer(bpy.types.Operator):
+    bl_idname = "bioxelnodes.slice_viewer"
+    bl_label = "Slice Viewer"
+    bl_description = "A preview scene setting for viewing slicers"
+    bl_icon = "FILE_VOLUME"
+
+    def execute(self, context):
+        bpy.context.scene.eevee.use_taa_reprojection = False
+        bpy.context.scene.eevee.volumetric_tile_size = '2'
+        bpy.context.scene.eevee.volumetric_shadow_samples = 128
+        bpy.context.scene.eevee.volumetric_samples = 128
+        bpy.context.scene.eevee.volumetric_ray_depth = 1
+        bpy.context.scene.eevee.use_volumetric_shadows = False
+
+        for area in bpy.context.screen.areas:
+            if area.type == 'VIEW_3D':
+                area.spaces[0].shading.type = 'MATERIAL'
+                area.spaces[0].shading.studio_light = 'studio.exr'
+                area.spaces[0].shading.studiolight_intensity = 2.5
+                area.spaces[0].shading.use_scene_lights = False
+                area.spaces[0].shading.use_scene_world = False
+
+        return {'FINISHED'}
+
+
+def get_all_layers(layer_filter=None):
+    def _layer_filter(layer_obj):
+        return True
+
+    layer_filter = layer_filter or _layer_filter
+    layer_objs = get_all_layer_objs()
+    return [obj for obj in layer_objs if layer_filter(obj)]
+
+
+class SaveAllLayersCache(bpy.types.Operator, SaveLayersCache):
+    bl_idname = "bioxelnodes.save_all_layers_cache"
+    bl_label = "Save All Layers Cache"
+    bl_description = "Save all cache of this file"
+    bl_icon = "FILE_TICK"
+
+    success_msg = "Successfully saved all layers."
+
+    def get_layers(self, context):
+        def is_not_missing(layer_obj):
+            return not is_missing_layer(layer_obj)
+        return get_all_layers(is_not_missing)
+
+
+class RemoveAllMissingLayers(bpy.types.Operator, RemoveLayers):
+    bl_idname = "bioxelnodes.remove_all_missing_layers"
+    bl_label = "Remove All Missing Layers"
+    bl_description = "Remove all current container missing layers"
+    bl_icon = "BRUSH_DATA"
+
+    success_msg = "Successfully removed all missing layers."
+
+    def get_layers(self, context):
+        def is_missing(layer_obj):
+            return is_missing_layer(layer_obj)
+        return get_all_layers(is_missing)
+
+    def invoke(self, context, event):
+        context.window_manager.invoke_confirm(self,
+                                              event,
+                                              message=f"Are you sure to remove all **Missing** layers?")
         return {'RUNNING_MODAL'}

bioxelnodes/operators/node.py

@@ -0,0 +1,60 @@
+import bpy
+
+from ..bioxelutils.common import is_incompatible, local_lib_not_updated
+from ..bioxelutils.node import assign_node_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 node library version does not match the current addon version, which may cause problems, please save the node library again.")
+
+        return {"FINISHED"}

bioxelnodes/operators/utils.py

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

bioxelnodes/preferences.py

@@ -1,6 +1,7 @@
 import bpy
 from pathlib import Path
 
+
 class BioxelNodesPreferences(bpy.types.AddonPreferences):
     bl_idname = __package__
 
@@ -10,14 +11,19 @@ class BioxelNodesPreferences(bpy.types.AddonPreferences):
         default=str(Path(Path.home(), '.bioxelnodes'))
     )  # type: ignore
 
-    do_change_render_setting: bpy.props.BoolProperty(
-        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",

docs/advanced.md

@@ -0,0 +1,3 @@
+# Advanced
+
+WIP

docs/color.md

@@ -1 +0,0 @@
-This type of node is responsible for setting the color properties of the shader

docs/concept.md

@@ -1,46 +0,0 @@
-# Concepts & Pipeline
-
-## Container, Layer, Component
-
-Bioxel Nodes imports volumetric data and put it into a **Container** as a **Layer**. One container may has more than one layer, and each layer stores the information of different fields under the same location, which is similar to the view layers in map app, except that here it is in 3D space.
-
-In order to visualize the volumetric data the way we want it to, we need to build renderable objects from layers. We call those objects **Component**. The following diagram shows the relationship of **Container**, **Layer**, and **Component**:
-
-![alt text](assets/features_concept.png)
-
-### Container Structure
-
-In Blender, container structure is like this:
-
-```bash
-Case_0000 # Container
-|-- Case_0000_CT # Layer
-|-- Case_0000_Label_1 # Layer
-`-- Case_0000_Label_2 # Layer
-```
-
-The container also stores the build process in geometry nodes:
-
-![alt text](assets/features_container.png)
-
-### Layer Type
-The layer is categorized into these by data type:
-
--   Scalar
--   Label
--   Vector (Not implemented yet)
--   Color (Not implemented yet)
-
-## Component Building Pipline
-
-In order to build a component, the general process is to first use a "Mask Method" node to build the surface of the component based on its layers, and then connect to a "Assign Shader" node to add the physical properties. Finally, if you need to cut the cross-section, then connect to a "Cut" node. The whole process is shown in the following diagram
-
-![alt text](assets/nodes_concept.png)
-
-A typical example looks like this:
-
-![alt text](assets/nodes_example.png)
-
-The "Mask Method" node tends to be very computationally intensive, and if it consumes too much time, then you can bake it with a "Bake" node after it (but you need to save the Blender file first).
-
-![alt text](assets/nodes_bake.png)

docs/cut.md

@@ -1 +0,0 @@
-This type of node is responsible for cutting components to present cross-section

docs/import.md

@@ -1,41 +0,0 @@
-
-## First Time Import Volume Data
-
-File > Import > Volume Data as Bioxel Layer
-
-### Resample
-
-![alt text](assets/features_resample.png)
-
-Sometimes the original data is too big, or the spacing in the original data is not reasonable, you can modify the `Bioxel Size` and `Original Spacing` to adjust the Shape of the layer.
-
-A bioxel is like a pixel, the larger the `Bioxel Size`, the lower the resolution of the image, Original Spacing will be read from the original data record, but sometimes the image doesn't have original spacing, you may need to input it manually to get the correct shape.
-
-### Read as
-
--   as Scalar
-
-    ![alt text](assets/features_as-scalar.png)
-
-    In some cases the environment value is higher than the value of the target object, you can check `Invert Scalar` to adjust the value for better result.
-
--   as Labels
-
-    Many AI segmentation task datasets, provide segmentation data, which are often an integer value representing a layer of segmentation labels. You can set it to `Labels` to load them.
-
--   _as Vector (Not implemented yet)_
-
--   _as Color (Not implemented yet)_
-
-### Others
-
-![alt text](assets/features_import-others.png)
-
-`Scene Scale` determines how many units of length in the Blender world correspond to one unit of length in the Bioxel world. Since Blender defaults to meters, and the default size of blender primitives are around 1 blender unit. Therefore `Scene Scale` set to 0.01 is appropriate.
-
-`Orient to RAS` determines whether the layer should be converted to the RAS coordinate system. Regardless of the format of the medical image data, the coordinate system is mostly the LPS coordinate system. Bioxel, however, are in the RAS coordinate system and therefore need to be transformed in most cases.
-
-## Adding Volume Data to an existing container
-
-In 3D view or outliner panel, select the container and right click, Bioxel Nodes > Add Volume Data to Container.
-The import settings are the same as for the first time import.

docs/improve_performance.md

@@ -0,0 +1,39 @@
+# Improve Performance
+
+Volume reconstruction and volume rendering are very consuming computation, I believe that this add-on's experience is terrible on poorly hardware. here are tips to improve the add-on performance.
+
+## Use Low-Res Data as Preview
+
+The addon provides data resample function, the operation is as follows. First, in the container's geometry node, select the layer you need to resample, right-click **Bioxel Nodes > Resample Value**, in the dialog box, change the "Bioxel Size" value to twice or more than the current value, click OK. the addon will create a low-res version of the layer and load it into the container's geometry node.
+
+![alt text](assets/improve_performance/image.png)
+
+You can see that the speed of the reconstruction has been reduced from 240 ms to 37 ms, making it possible to compute in almost real-time, and improving the speed of the feedback of the changing the parameters. Once you are satisfied with the adjustment, you can then connect the original layer to the nodes. This tip can greatly improve the operation experience of the node.
+
+## Raise the Step Rate of a Container
+
+Step rate is a key setting in volume rendering. The higher the step rate, the faster the rendering will be, but at the same time, the thinner the volume will look. If you want to have a very thin effect, or if you don't need to cut through component, you can always set the step rate high, you can adjust step rate in the render settings globaly. However, I recommend you to adjust the step rate of the container separately, so that it doesn't affect the rendering of the other volume in the Blender file, do as follows.
+
+In the container's geometry nodes panel menu, click **Bioxel Nodes > Change Container Properties**, in the dialog box, raise the "Step Rate" value (up to 100) and click OK.
+
+![alt text](assets/improve_performance/image-1.png)
+
+You can see that the rendering speed is much higher, but at the same time the cuts look blurry and transparent.
+
+## Balance rendering settings
+
+I list some of the settings that affect the volume rendering most, so you can find the most balanced settings for your needs.
+
+-   **Light Paths > Max Bounces > Volume** affects the number of bounces a volume has, the higher the value, the more transparent it will look.
+
+-   **Light Paths > Max Bounces > Transparent** affects the number of times transparent surfaces are transmitted, the higher the value, the more transparent it will look.
+
+-   **Volumes > Step Rate Render | Viewport** affects the volume rendering step, the smaller the value, the more detailed the volume will look
+
+Bioxel Nodes provides some render setting presets for quick setup. In the top menu, click **Bioxel Nodes > Render Setting Presets**, including Performance (left), Balance (center), and Quality (right). Here is a comparison of them.
+
+![alt text](assets/improve_performance/image-2.png)
+
+## Rendering with EEVEE
+
+EEVEE doesn't render volume as well as Cycles, but it does have the advantage of rendering the volumetric data, and is even a better choice if you want to get a clear view of slice. And EEVEE's real-time rendering make it possible to create interactive stuff in Blender.

docs/index.md

@@ -1,4 +1,4 @@
-[中文文档](https://uj6xfhbzp0.feishu.cn/wiki/Qx3VwHuNPimeI8kr6nDcvl1DnHf?from=from_copylink)
+[中文文档](https://uj6xfhbzp0.feishu.cn/wiki/LPKEwjooSivxjskWHlCcQznjnNf?from=from_copylink)
 
 # Bioxel Nodes
 
@@ -26,18 +26,18 @@ Welcome to our [discord server](https://discord.gg/pYkNyq2TjE), if you have any
 
 ## Support Multiple Formats
 
-| Format | EXT                                      | Test    |
-| ------ | ---------------------------------------- | ------- |
-| DICOM  | .dcm, .DCM, .DICOM, .ima, .IMA           | ✅ pass |
-| BMP    | .bmp, .BMP                               | ✅ pass |
-| JPEG   | .jpg, .JPG, .jpeg, .JPEG                 | ✅ pass |
-| PNG    | .png, .PNG                               | ✅ pass |
-| TIFF   | .tif, .TIF, .tiff, .TIFF                 | ✅ pass |
-| Nifti  | .nia, .nii, .nii.gz, .hdr, .img, .img.gz | ✅ pass |
-| Nrrd   | .nrrd, .nhdr                             | ✅ pass |
-| HDF5   | .hdf, .h4, .hdf4, .he2, .h5, .hdf5, .he5 | ✅ pass |
-| OME    | .ome.tiff, .ome.tif                      | ✅ pass |
-| MRC    | .mrc, .mrc.gz, .map, .map.gz             | ✅ pass |
+| Format | EXT                                      |
+| ------ | ---------------------------------------- |
+| DICOM  | .dcm, .DCM, .DICOM, .ima, .IMA           |
+| BMP    | .bmp, .BMP                               |
+| JPEG   | .jpg, .JPG, .jpeg, .JPEG                 |
+| PNG    | .png, .PNG                               |
+| TIFF   | .tif, .TIF, .tiff, .TIFF                 |
+| Nifti  | .nia, .nii, .nii.gz, .hdr, .img, .img.gz |
+| Nrrd   | .nrrd, .nhdr                             |
+| HDF5   | .hdf, .h4, .hdf4, .he2, .h5, .hdf5, .he5 |
+| OME    | .ome.tiff, .ome.tif                      |
+| MRC    | .mrc, .mrc.gz, .map, .map.gz             |
 
 ## Support 4D volumetric data
 
@@ -59,16 +59,6 @@ Welcome to our [discord server](https://discord.gg/pYkNyq2TjE), if you have any
 -   Only works with Cycles CPU , Cycles GPU (OptiX), EEVEE
 -   Section surface cannot be generated when convert to mesh (will be supported soon)
 
-## Compatible to Newer Version
-
-**v0.3.x is not compatible to v0.2.x, Updating this addon may break old files. Read the following carefully before upgradation**
-
-Before upgradation, you need to ask yourself whether this project file will be modified again or not, if it's an archived project file, I would recommend that you run **Bioxel Nodes > Save Staged Data** to make the addon nodes permanent. In this way, there will be no potential problem with the nodes not functioning due to the addon update.
-
-After the addon update, your old project files may not work either, this may be because you had executed **Save Staged Data**. If so, you need to execute **Bioxel Nodes > Relink Nodes to Addon** to relink them to make sure that the addon's new functionality and the addon nodes are synchronized.
-
-Also, the older shaders are not based on OSL, so if you find that you can't render volumes, you need to turn on **Open Shading Language (OSL)** in the Render Settings.
-
 ## Roadmap
 
 -   Better multi-format import experience

docs/installation.md

@@ -1,27 +1,19 @@
 # Installation
 
-> **Currently only support Blender 4.1 or above, make sure you have the correct version of Blender.**
+**Currently only support Blender 4.2 or above, make sure you have the correct version of Blender.**
 
-## For Blender 4.2 or higher
+## Install in Blender (recommended)
 
-The most recommended way is to open **Edit > Preferences > Extension**, enter "bio" in the search box and click **Install**. since the addon is quite large (20MB) you may need to wait a while!
+This is the most recommended way, in the top menu, click **Edit > Preferences**, in "Get Extensions" Section, enter "bio" in the search box, then click Install. due to the add-on size (25MB~50MB) you may need to wait a while.
 
-![extension](assets/installation_extension.png)
+![alt text](assets/installation/image.png)
 
-Thats it!
+## Blender Official Extensions Website
 
-> If it cannot be enable, reboot blender or install again as administrator
+Or you can visit the Blender official extensions website at [https://extensions.blender.org/add-ons/bioxelnodes/](https://extensions.blender.org/add-ons/bioxelnodes/)
+Click Get Add-on, open Blender, drag in Blender and follow the instructions to install.
 
-Also, you can do it maually. Download the **Extension** version `BioxelNodes_Extension_{version}.zip` from https://github.com/OmooLab/BioxelNodes/releases/latest  
-In Blender, **Edit > Preferences > Extensions > Install from Disk**, select the zip file you just downloaded.
+## Manual Install
 
-## For Blender 4.1
-
-Download the **Addon** version `BioxelNodes_Addon_{version}.zip` from https://github.com/OmooLab/BioxelNodes/releases/latest  
-In Blender, Edit > Preferences > Add-ons > Install, select the zip file you just downloaded.
-
-The add-on requires a third-party python dependency called SimpleITK, click `Install SimpleITK` button below to install the dependency. After clicking, blender may get stuck, it is downloading and installing, just wait for a moment. After that, click `Reboot Blender` button.
-
-![dependency](assets/installation_dependency.png)
-
-This step may have failed due to network factors, just click "Set PyPI Mirror" to change the mirror.
+You can also install _BioxelNodes\_{version}.zip_ manually by downloading from [bere](https://github.com/OmooLab/BioxelNodes/releases/latest).
+In the top menu, click **Edit > Preferences**, **Add-ons > Install from Disk** and select the Zip file you just downloaded.

docs/mask.md

@@ -1 +0,0 @@
-This type of node is responsible for culling out the extent of the component that does not need to be rendered, forming the interface between the object and the object, or the surface of the object (i.e., the interface between the object and the air)

docs/nodes.md

@@ -1,350 +0,0 @@
-# Nodes
-
-## Mask Methods
-
-### ⬆️ Mask by Threshold
-
-<div class="grid cards" markdown>
-
--   ![alt text](assets/nodes_mask-by-threshold.png)
-
--   Generate a mask by keeping only the positions that exceed the threshold (this only works with scalar)
-
-    ***
-
-    Node Parameter:
-
-    -   **Layer**, _the input scalar_
-    -   **Threshold**, _the threshold value_
-    -   Preview
-        -   **Detail Factor**, _the fineness of the preview, the larger the factor, the coarser preview is_
-    -   (Label Mask)
-        -   **Layer**, _the input label_
-        -   **Invert**, _invert mask_
-        -   **Sample Size**, _the mask sample size_
-    -   (Replacement)
-        -   **Joined**, _the joined layer_
-
-</div>
-
-### ↕ Mask by Range
-
-<div class="grid cards" markdown>
-
--   ![alt text](assets/nodes_mask-by-range.png)
-
--   Generate a mask by keeping only the positions that in range (this only works with scalar)
-
-    ***
-
-    Node Parameter:
-
-    -   **Layer**, _the input scalar_
-    -   **Fram Min**, _the lower limit_
-    -   **Fram Max**, _the upper limit_
-    -   Preview
-        -   **Detail Factor**, _the fineness of the preview, the larger the factor, the coarser preview is_
-    -   (Label Mask)
-        -   **Layer**, _the input label_
-        -   **Invert**, _invert mask_
-        -   **Sample Size**, _the mask sample size_
-    -   (Replacement)
-        -   **Joined**, _the joined layer_
-
-</div>
-
-### 🔤 Mask by Label
-
-<div class="grid cards" markdown>
-
--   ![alt text](assets/nodes_mask-by-label.png)
-
--   Generate a mask by keeping only the positions that in label (this only works with label)
-
-    ***
-
-    Node Parameter:
-
-    -   **Layer**, _the input label_
-    -   Preview
-        -   **Detail Factor**, _the fineness of the preview, the larger the factor, the coarser preview is_
-    -   (Replacement)
-        -   **Joined**, _the joined layer_
-
-</div>
-
-## Shaders
-
-### 🥚 Solid Shader
-
-<div class="grid cards" markdown>
-
--   ![alt text](assets/nodes_solid-shader.png)
-
--   Assign a opaque shader based on a preview mesh with no inclusions visible. Fastest rendering speed. Does not support cross-section and color ramp.
-
-    ***
-
-    Node Parameter:
-
-    -   **Component**, _the upstream component_
-        -   Base
-        -   **Color**, _albedo or emission color_
-        -   **Subsurface**, _the subsurface scale_
-        -   **Opacity**, _the opacity of all_
-    -   Specular
-        -   **Specular**, _the specular of surface_
-        -   **Roughness**, _the roughness of surface_
-    -   Emission
-        -   **Emission**, _the emission strength_
-
-</div>
-
-### 🦠 Slime Shader
-
-<div class="grid cards" markdown>
-
--   ![alt text](assets/nodes_slime-shader.png)
-
--   Assign a semi-transparent shader based on the preview mesh with visible inclusions. Does not support cross-section and color ramp.
-
-    ***
-
-    Node Parameter:
-
-    -   **Component**, _the upstream component_
-    -   Base
-        -   **Color**, _albedo or emission color_
-        -   **Density**, _the degree of solidity_
-        -   **Anisotropy**, _the anisotropy of scatting_
-    -   Specular
-        -   **Specular**, _the specular of surface_
-        -   **Roughness**, _the roughness of surface_
-    -   Emission
-        -   **Emission**, _the emission strength_
-
-</div>
-
-### ☁️ Volume Shader
-
-<div class="grid cards" markdown>
-
--   ![alt text](assets/nodes_volume-shader.png)
-
--   Assign a volume-based shader with support for cross-section and color ramp.
-
-    ***
-
-    Node Parameter:
-
-    -   **Component**, _the upstream component_
-    -   Base
-        -   **Color**, _albedo or emission color_
-        -   **Density**, _the degree of solidity_
-        -   **Anisotropy**, _the anisotropy of scatting_
-    -   Emission
-        -   **Emission**, _the emission strength_
-
-</div>
-
-### 🔬 Universal Shader
-
-<div class="grid cards" markdown>
-
--   ![alt text](assets/nodes_universal-shader.png)
-
--   Assign a ultimate shader, supporting all features of Bioxel Nodes. Of course, the price is slow rendering, which can be greatly improved by adjusting the Volumes > Step Rate to 100 in the Render Settings Panel.
-
-    ***
-
-    Node Parameter:
-
-    -   **Component**, _the upstream component_
-    -   Base
-        -   **Color**, _albedo or emission color_
-        -   **Density**, _the degree of solidity_
-        -   **Anisotropy**, _the anisotropy of scatting_
-    -   Specular
-        -   **Specular**, _the specular of surface_
-        -   **Roughness**, _the roughness of surface_
-    -   Emission
-        -   **Emission**, _the emission strength_
-
-</div>
-
-## Cutters
-
-### 🪚 Cut
-
-<div class="grid cards" markdown>
-
--   ![alt text](assets/nodes_cut.png)
-
--   Execute all cutters on one component.
-
-    ***
-
-    Node Parameter:
-
-    -   **Component**, _the upstream component_
-    -   **Cutter 0~4**, _the cutters_
-    -   **Hide Guide**, _hide the cutter guide_
-
-</div>
-
-
-### 🧀 Plane Object Cutter
-
-<div class="grid cards" markdown>
-
--   ![alt text](assets/nodes_plane-object-cutter.png)
-
--   Also a plane cutter, but origin and direction are based on exist object.
-
-    ***
-
-    Node Parameter:
-
-    -   **Plane**, _the plane object_
-    -   Guide
-        -   **Show**, _show the cutter guide_
-        -   **Scale**, _scale the cutter guide_
-
-</div>
-
-## Colors
-
-### 🎨 Color Presents
-
-<div class="grid cards" markdown>
-
--   ![alt text](assets/nodes_color-presets.png)
-
--   Set color from presets.
-
-    ***
-
-    Node Parameter:
-
-    -   **Component**, _the upstream component_
-    -   **Presets**, _select color presents_
-    -   **Fram Min**, _ramp factor lower limit_
-    -   **Fram Max**, _ramp factor upper limit_
-
-</div>
-
-### 2️⃣ Color Ramp 2
-
-<div class="grid cards" markdown>
-
--   ![alt text](assets/nodes_color-ramp-2.png)
-
--   Set color ramp base on scalar value.
-
-    ***
-
-    Node Parameter:
-
-    -   **Component**, _the upstream component_
-    -   **Fram Min**, _ramp factor lower limit_
-    -   **Fram Max**, _ramp factor upper limit_
-    -   Ramp
-        -   **Pos0 Color**, _position 0% Color_
-        -   **Pos1 Color**, _position 100% Color_
-        -   **Gamma**, _non-linear coefficient, the larger the coefficient, the more lower value color_
-        -   **Contrast**, _the larger the contrast, the harder color ramp will be_
-
-</div>
-
-### 3️⃣ Color Ramp 3
-
-<div class="grid cards" markdown>
-
--   ![alt text](assets/nodes_color-ramp-3.png)
-
--   Set color ramp base on scalar value.
-
-    ***
-
-    Node Parameter:
-
-    -   **Component**, _the upstream component_
-    -   **Fram Min**, _ramp factor lower limit_
-    -   **Fram Max**, _ramp factor upper limit_
-    -   Ramp
-        -   **Pos0 Color**, _position 0% Color_
-        -   **Pos1 Color**, _position 50% Color_
-        -   **Pos2 Color**, _position 100% Color_
-        -   **Gamma**, _non-linear coefficient, the larger the coefficient, the more lower value color_
-        -   **Contrast**, _the larger the contrast, the harder color ramp will be_
-
-</div>
-
-### 4️⃣ Color Ramp 4
-
-<div class="grid cards" markdown>
-
--   ![alt text](assets/nodes_color-ramp-4.png)
-
--   Set color ramp base on scalar value.
-
-    ***
-
-    Node Parameter:
-
-    -   **Component**, _the upstream component_
-    -   **Fram Min**, _ramp factor lower limit_
-    -   **Fram Max**, _ramp factor upper limit_
-    -   Ramp
-        -   **Pos0 Color**, _position 0% Color_
-        -   **Pos1 Color**, _position 33.3% Color_
-        -   **Pos2 Color**, _position 66.6% Color_
-        -   **Pos3 Color**, _position 100% Color_
-        -   **Gamma**, _non-linear coefficient, the larger the coefficient, the more lower value color_
-        -   **Contrast**, _the larger the contrast, the harder color ramp will be_
-
-</div>
-
-### 5️⃣ Color Ramp 5
-
-<div class="grid cards" markdown>
-
--   ![alt text](assets/nodes_color-ramp-5.png)
-
--   Set color ramp base on scalar value.
-
-    ***
-
-    Node Parameter:
-
-    -   **Component**, _the upstream component_
-    -   **Fram Min**, _ramp factor lower limit_
-    -   **Fram Max**, _ramp factor upper limit_
-    -   Ramp
-        -   **Pos0 Color**, _position 0% Color_
-        -   **Pos1 Color**, _position 25% Color_
-        -   **Pos2 Color**, _position 50% Color_
-        -   **Pos3 Color**, _position 75% Color_
-        -   **Pos4 Color**, _position 100% Color_
-        -   **Gamma**, _non-linear coefficient, the larger the coefficient, the more lower value color_
-        -   **Contrast**, _the larger the contrast, the harder color ramp will be_
-
-</div>
-
-## Utils
-
-### 📦 Join Component
-
-<div class="grid cards" markdown>
-
--   ![alt text](assets/nodes_join-component.png)
-
--   Components' combination should not be done by "Join Geometry" node because Blender Cycles can't render volumes in the same position, so the node will slightly offset all components randomly to avoid this problem.
-
-    ***
-
-    Node Parameter:
-
-    -   **Component 0~4**, _the components_
-
-</div>

docs/prepare_data.md

@@ -1,45 +0,0 @@
-# Prepare Your Data
-
-## Support Formats
-
-First thing first, you need to get your volumetric data ready in disk. Bioxel Nodes is developed based on Simple ITK, so theoretically all formats supported by Simple ITK are supported by the addon. If your data is not in the support list, you may do the data conversion first.
-
-| Format | EXT                                      | Test    |
-| ------ | ---------------------------------------- | ------- |
-| DICOM  | .dcm, .DCM, .DICOM, .ima, .IMA           | ✅ pass |
-| BMP    | .bmp, .BMP                               | ✅ pass |
-| JPEG   | .jpg, .JPG, .jpeg, .JPEG                 | ✅ pass |
-| PNG    | .png, .PNG                               | ✅ pass |
-| TIFF   | .tif, .TIF, .tiff, .TIFF                 | ✅ pass |
-| Nifti  | .nia, .nii, .nii.gz, .hdr, .img, .img.gz | ✅ pass |
-| Nrrd   | .nrrd, .nhdr                             | ✅ pass |
-| Meta   | .mha, .mhd                               | yet     |
-| HDF5   | .hdf, .h4, .hdf4, .he2, .h5, .hdf5, .he5 | ✅ pass |
-| VTK    | .vtk                                     | yet     |
-| BioRad | .PIC, .pic                               | yet     |
-| Gipl   | .gipl, .gipl.gz                          | yet     |
-| LSM    | .lsm, .LSM                               | yet     |
-| MINC   | .mnc, .MNC                               | yet     |
-| MRC    | .mrc, .rec                               | yet     |
-| OME    | .ome.tiff, .ome.tif                      | ✅ pass |
-| MRC    | .mrc, .mrc.gz, .map, .map.gz             | ✅ pass |
-
-## Download Data from Internet
-
-If you don't have any volumetric data, you can access open research data from list below.
-
-> Note that just because they are open and available for download does not mean you can use them for anything! Be sure to look at the description of the available scopes from website.
-
-| Source                                                                               | Object             |
-| ------------------------------------------------------------------------------------ | ------------------ |
-| [MorphoSource](https://www.morphosource.org/)                                        | Open Research Data |
-| [Dryad](https://datadryad.org)                                                       | Open Research Data |
-| [Cell Image Library](http://cellimagelibrary.org/home)                               | Cells              |
-| [OpenOrganelle](https://openorganelle.janelia.org/datasets)                          | Cells              |
-| [Allen Cell Explorer](https://www.allencell.org/3d-cell-viewer.html)                 | Cells              |
-| [EMDB](https://www.ebi.ac.uk/emdb/)                                                  | Protein, Viruses   |
-| [Embodi3D](https://www.embodi3d.com/files/category/37-medical-scans/)                | Medical Images     |
-| [Github](https://github.com/sfikas/medical-imaging-datasets)                         | Medical Images     |
-| [NIHR](https://nhsx.github.io/open-source-imaging-data-sets/)                        | Medical Images     |
-| [Medical Segmentation Decathlon](http://medicaldecathlon.com/)                       | Medical Images     |
-| [Visible Human Project](https://www.nlm.nih.gov/research/visible/visible_human.html) | Medical Images     |

docs/qa.md

@@ -0,0 +1,15 @@
+# Q & A
+
+## Nothing in the scene when rendering?
+
+If you're using the Cycles renderer with GPU, make sure your GPU supports "Optix", as Bioxel Nodes relies on OSL (Open shader language) for volumetric rendering, otherwise you'll have to use the CPU for rendering.
+
+If you're using the EEVEE renderer, this issue is due to EEVEE not loading shaders for some unknown reason, save the file and restart Blender to fix it.
+
+## After updating the addon, the nodes in the file have turned red?
+
+This is because the version of the nodes in the file does not match the current version of the addon after updating.
+
+If you still want to edit the file with Bioxel Nodes, you can only roll back the addon version to the version that corresponds to the nodes.
+
+If you just want the file to work and you won't rely on Bioxel Nodes any more, then you can just click **Bioxel Nodes > Relink Node Library >** in the top menu and select the corresponding version. Check to see if the nodes are working and rendering properly, and when everything is OK, click **Bioxel Nodes > Save Node Library** and select the save location in the dialog box.

docs/shader.md

@@ -1 +0,0 @@
-This type of node is responsible for setting material physical properties to the component to reflect the differences in rendering effects of different components.

docs/step_by_step.md

@@ -1,54 +1,101 @@
 # Step by Step
 
-## 1. Import Volumetric Data
+## Download Data
 
-**Bioxel Nodes > Import Volumetric Data (Init) > as Scalar**, select the data file, click on **Import as Scalar**. If the data is a sequence of files in directory, just pick **one** file in that directory, not the whole directory or multiple selection of files.
+Here is the open data from [Visible Human Project (VHP)](https://www.nlm.nih.gov/research/visible/visible_human.html) for you to learn how to use this addon. It is a CT scan image of a male head, download and unzip it to any location for later usage.
 
-> you can also drag one of the data file directly into the 3D viewport to trigger the importing
+[VHP_M_CT_Head.zip](https://drive.google.com/file/d/1kcnEwwDj-5X4U8330G_FNfWFS8f-892R/view?usp=sharing)
 
-![importing](assets/getting-started_importing.png)
+VHP original radiology data was shared in the proprietary format that predated DICOM, complicating its use. Now all data has been harmonized to standard DICOM and released in [NCI Imaging Data Commons (IDC)](https://portal.imaging.datacommons.cancer.gov/), you also can download data from IDC by yourself.
 
-It may take a while to read data. After finishing reading, it will pop up a dialog box. Ignore all the options, just click OK (we will talk about them later).
+## Import Data
 
-After the importing, the add-on will automatically add the necessary nodes to build the preview.
+In the top menu, click **Bioxel Nodes > Import Volumetric Data (Init) > as Scalar**, locate to the unzipped folder, select any DICOM file (don't select more than one, and don't select the folder either), and click **Import as Scalar**.
 
-![masking](assets/getting-started_masking.png)
+![alt text](assets/step_by_step/image.png)
 
-If there is nothing in the bbox wireframe, select the wireframe in 3D viewport, open the geometry nodes panel, set **Threshold** in the node lower to modify the preview.
+You can also choose to import data by dragging one DICOM file into the 3D viewport (some DICOM files don't have extension suffix and can't be dragged in).
 
-## 2. Shading the Structure
+The process of reading the data may take a while, the bottom right corner of the Blender interface will show you the progress of the reading, and a dialog box will pop up when the reading is successful. Ignore all the options for now and just click OK, I will explain the purpose of these options later.
 
-The only node "Scalar" is responsible for mask out the unwanted area and generate the structure surface. You need to assign a shader to truly see the structure, connect a **Slime Shader** node (**Add > Bioxel Nodes > Shaders > Slime Shader**) after it. Turned on the cycles rendering to see the result.
+The import process involves data conversion, so there is more waiting time, and the progress of the import is displayed in the lower right corner of the interface. After importing, the addon will create a new object, with a new geometry nodes that will serve as a "workbench" for manipulating the data, the new object is called the **Container**. The newly imported data is stored in the Container as a **Layer**, which is loaded into the Container's Geometry node via the "Fetch Layer" node (the red one), and be converted into a **Component** that can be rendered.
 
-![shading](assets/getting-started_shading.png)
+![alt text](assets/step_by_step/image-1.png)
 
-You may change the **Color**, **Density** to modify the shader effect. All the parameters are straightforward, you can understand them by changing their values.
+Next, let's preview the data in Blender.
 
-## 3. Cut to Cross-section
+In the container's geometry nodes panel menu, click **Bioxel Nodes > Add a Slicer**. The addon will insert a node named "Slice" between the "Fetch Layer" and the "Output" and create a new plane object named "Slicer". Click the "Slice Viewer" button in the upper right corner of the 3D viewport to enter the preview mode, then move and rotate the "Slicer" object. You will see a slice image of the data, which should be familiar to anyone who has used any DICOM viewing software.
 
-We often need to cut the structure to see the inside of the volumetric data. With Bioxel Nodes, it can be done by one click: select the structure in 3D viewport, right click, **Bioxel Nodes > Add a Plane Cutter**
-. The add-on will add a cut node and a cutter object node to the node graph, which are responsible for the cutting process.
+![alt text](assets/step_by_step/image-2.png)
 
-![cutting](assets/getting-started_cutting.png)
+(If the volume disappears when you click the "Slice Viewer" button, save the file and restart Blender, it should be fixed, or you can turn on the Cycles rendering to see the slicer plane as well. The issue is caused by EEVEE's failure of reloading the shaders.)
 
-> Change the shader from **Slime** to **Universal** to render the cross-section. But it will increase rendering time
+The "Slicer" node is used to display the slices of the data, with an external object as the location of the slice plane. This step is not necessary for visualization, but it provides a quick way to preview the data in Blender for user perception. Next, let's turn the volumetric data into a renderable object.
 
-## 4. Save Staged Data (Optional)
+## Cutout the skull
 
-The VDB cache and the custom nodes are not reachable to other computers if you don't save them. Those staged data should be saved, If you want to give your blender file to someone else, or you want to archive your blender file.
+Bone tends to have much higher CT values than soft tissue, so you can split bone and soft tissue by setting a threshold. In the Geometry Nodes panel menu of the container, click **Add > Bioxel Nodes > Component > Cutout by Threshold** to add a "Cutout" node and connect it between the "Fetch Layer" node and the "Output", and then set the "Threshold" parameter of the "Cutout by Threshold" node to 0.3 and turn on the "With Surface" option. Switch to viewport shading to "Render Preview". The node graph and the render result are shown below.
 
-Save your blender file, then just click **Bioxel Nodes > Save Staged Data**
+![alt text](assets/step_by_step/image-3.png)
 
-![save staged data](assets/getting-started_save_staged_data.png)
+If you want the render result to be consistent with the above image, you also need to change the default light object type from "Point" to "Area" to increase the brightness, and change the Look in Color Management to "High Contrast".
 
-Just click **OK**, after that, both the VDB cache and the custom nodes are restored in relative locations. When you share this file with someone, pack the entire directory so that the resources will be not lost. The other person will be able to open it correctly, regardless of whether they have Bioxel Nodes installed or not.
+You can understand the role of the "Threshold" parameter in shaping the output by changing it. If you feel very laggy while draging the parameter, you can temporarily turn off the "With Surface" option in the "Cutout" node. When you are satisfied, turn it on again. In addition, the volume rendering is very computationally intensive, which is also a major cause of the lag, so you can adjust the parameters in "Slice Viewer" mode first, and then do the Cycles rendering when you are satisfied.
 
-## 5. Convert to Editable Mesh (Optional)
+You may consider using GPU for faster rendering, but please note that Bioxel Nodes only supports Optix GPUs due to its dependency on OSL (Open shader language), and the first time you turn on GPU rendering, you may need to wait for Blender to load the appropriate dependencies (the screen will get stuck), so please be patient.
 
-If you want digital sculpting, 3D printing, exporting to game engine, you should convert to editable mesh first.
+Although the output component looks like a mesh object, it retains its internal information through its volume, so when you cut through the component, you should see an inhomogeneous cross-section made up of volume, rather than just an empty shell like any mesh object. Let's cut the skull to see its complex internal structure.
 
-Select the wireframe in 3D viewport, right click **Bioxel Nodes > Pick Mesh**.
+## Cut and Color
 
-![to mesh](assets/getting-started_convert_to_mesh.png)
+In the container's geometry nodes panel menu, click **Bioxel Nodes > Add a Cutter > Plane Cutter**, the addon will insert a "Cut" node and a "Object Cutter" node. Also, it will create a new plane object named "Plane Cutter" to the scene, at this point you should be able to see that the skull has been cut through as expected.
 
-It will create a new object with geometry nodes to refer the mesh. You can apply the geometry node to break the connection.
+Just like the "Slicer" object, move and rotate the "Plane Cutter" and the position and direction of the cut will change accordingly. Please adjust the Cutter object to a vertical orientation so that it cuts the skull vertically, as shown below.
+
+![alt text](assets/step_by_step/image-4.png)
+
+The CT value of the skull is inhomogeneous, which reflects the difference in substance density of the bone. We can enhance the display of this difference by coloring. In the Geometry Nodes panel menu of the container, click **Add > Bioxel Nodes > Propetry > Set Color by Ramp 5** to add the "Set Color" node and connect it after any node. Set the node's parameters "From Min" to 0.3 and "From Max" to 0.5, as shown below.
+
+![alt text](assets/step_by_step/image-5.png)
+
+When rendering is turned on, you can clearly see that the calvaria and teeth are colored red, meaning that the bone in these areas is denser. You can try to adjust the parameters of the "Set Color" node to recognize their roles. If you feel laggy when draging the parameters, you can temporarily turn off "With Surface" and switch to "Slice Viewer" mode.
+
+## Transformation
+
+You may find that the position of the skull is a bit off the origin, this is due to the fact that the addon keeps the position information from the original data record during the import process. If you need to change the position, do not move the container (object) directly as you would in 3D viewport; the addon provides dedicated "Transform" node to handle transformations.
+
+In the Geometry Nodes panel menu of the container, click **Bioxel Nodes > Add a Locator**, the addon will insert the "Transform Parent" node and create a new empty object named "Locator". If you move, rotate, or scale the "Locator", the skull will Transform as well. If you also want the origin of the rotational transformation to be set at the geometric center of the skull, just add a "ReCenter" node (Add > Bioxel Nodes > Transform > ReCenter) in front of the "Transform Parent" node, as shown below.
+
+![alt text](assets/step_by_step/image-6.png)
+
+Being used to moving objects directly in the 3D viewport, you may find it strange to have an extra step to transform component like this. This is in consideration of the fact that there may be multiple components involved in one container with different transform needs, as well as future development plans for resampling mechanism, which I'll explain in more detail later.
+
+## Surface Mesh
+
+A mesh, made up of vertexs and faces, is the "greatest common" in the 3D world. Therefore, in order to be compatible with other 3D workflow, the addon provides the "To Surface" node (Add > Bioxel Nodes > Component > ToSurface), which converts the component into a mesh. Note that the surface mesh is not editable in the container's geometry node, and can only be connected to "Transform" and "Shader" nodes.
+
+As shown below, you can connect "Slime Shader" node (Add > Bioxel Nodes > Surface > Slime Shader) after the "To Surface" node to give the surface a shader, or connect "Transform" nodes.
+
+![alt text](assets/step_by_step/image-7.png)
+
+If you want to edit the mesh, click **Bioxel Nodes > Extract from Container > Extract Surface** in the Geometry Nodes panel menu of the container. The addon will create a new object with Geometry Nodes, in which a "Fetch Surface" node to read the surface mesh. You can apply this geometry node to edit the mesh as usual. Or you can leave the geometry node in place and keep it connected to the original container in real time.
+
+![alt text](assets/step_by_step/image-8.png)
+
+(To show it better, I made an X-axis offset to the newly created mesh, otherwise the container and the mesh are perfectly overlapping.)
+
+## Save Temporary Files
+
+The layers cache is stored in a temporary folder, while the addon's custom nodes are linked to the node library file in addon directory. Both of them are exist locally by default, and if you only deliver the Blender file to other devices, the file will not work properly because the resources are missing.
+
+Therefore, you need to save all temporary files before you deliver the Blender file. The procedure is simple:
+
+1. Save the Blender file.
+2. in the top menu, click **Bioxel Nodes > Save Node Library**, and set the relative path.
+3. in the top menu, click **Bioxel Nodes > Save All Layers Cache** and set the relative path.
+
+Zip the Blender file together with the local node library file and the layer cache files (there may be more than one).
+
+![alt text](assets/step_by_step/image-9.png)
+
+🤗 If you can follow the documentation up to this point, you're already started!

docs/support_format.md

@@ -0,0 +1,39 @@
+# Support Format
+
+Can't wait to play with the addon using your own data? Here's a list of the formats currently supported.
+
+| Format | EXT                                      |
+| ------ | ---------------------------------------- |
+| DICOM  | .dcm, .DCM, .DICOM, .ima, .IMA           |
+| BMP    | .bmp, .BMP                               |
+| JPEG   | .jpg, .JPG, .jpeg, .JPEG                 |
+| PNG    | .png, .PNG                               |
+| TIFF   | .tif, .TIF, .tiff, .TIFF                 |
+| Nifti  | .nia, .nii, .nii.gz, .hdr, .img, .img.gz |
+| Nrrd   | .nrrd, .nhdr                             |
+| HDF5   | .hdf, .h4, .hdf4, .he2, .h5, .hdf5, .he5 |
+| OME    | .ome.tiff, .ome.tif                      |
+| MRC    | .mrc, .mrc.gz, .map, .map.gz             |
+
+Despite my best efforts, I still can't achieve perfect support for all volumetric data formats, and I will continue to work on this.
+
+## Open Databases
+
+If you don't have volumetric data, then you can download from some open databases.
+
+**Note that just because they are open and available for download does not mean you can use them for anything! Be sure to look at the description of the available scopes from website.**
+
+| Source                                                                               | Object             |
+| ------------------------------------------------------------------------------------ | ------------------ |
+| [MorphoSource](https://www.morphosource.org/)                                        | Open Research Data |
+| [Dryad](https://datadryad.org)                                                       | Open Research Data |
+| [Cell Image Library](http://cellimagelibrary.org/home)                               | Cells              |
+| [OpenOrganelle](https://openorganelle.janelia.org/datasets)                          | Cells              |
+| [Allen Cell Explorer](https://www.allencell.org/3d-cell-viewer.html)                 | Cells              |
+| [EMDB](https://www.ebi.ac.uk/emdb/)                                                  | Protein, Viruses   |
+| [IDC](https://portal.imaging.datacommons.cancer.gov/explore/)                        | Medical Images     |
+| [Embodi3D](https://www.embodi3d.com/files/category/37-medical-scans/)                | Medical Images     |
+| [Github](https://github.com/sfikas/medical-imaging-datasets)                         | Medical Images     |
+| [NIHR](https://nhsx.github.io/open-source-imaging-data-sets/)                        | Medical Images     |
+| [Medical Segmentation Decathlon](http://medicaldecathlon.com/)                       | Medical Images     |
+| [Visible Human Project](https://www.nlm.nih.gov/research/visible/visible_human.html) | Medical Images     |