fix: relocate cannot work on missing layer

fix: import fail if label are all zero
fix: add cutter name to node
fix: cannot append node lib file on NAS (UNC path)
fix: join component cause disappear
feat: smooth label
feat: better topo on cutout by range

bioxelnodes/bioxel/layer.py

@@ -77,7 +77,7 @@ def fill(self, value: float, mask: np.ndarray, smooth: int = 0):
             for f in range(self.frame_count):
                 mask_frame = mask[f, :, :, :]
                 if smooth > 0:
-                    mask_frame = scipy.minimum_filter(mask_frame.astype(np.float32),
+                    mask_frame = scipy.median_filter(mask_frame.astype(np.float32),
                                                       mode="nearest",
                                                       size=smooth)
                 # mask_frame = scipy.median_filter(
@@ -87,7 +87,7 @@ def fill(self, value: float, mask: np.ndarray, smooth: int = 0):
             for f in range(self.frame_count):
                 mask_frame = mask[:, :, :]
                 if smooth > 0:
-                    mask_frame = scipy.minimum_filter(mask_frame.astype(np.float32),
+                    mask_frame = scipy.median_filter(mask_frame.astype(np.float32),
                                                       mode="nearest",
                                                       size=smooth)
                 # mask_frame = scipy.median_filter(
@@ -119,10 +119,6 @@ def resize(self, shape: tuple, smooth: int = 0, progress_callback=None):
             if progress_callback:
                 progress_callback(f, self.frame_count)
 
-            # frame = ski.resize(data[f, :, :, :],
-            #                    shape,
-            #                    preserve_range=True,
-            #                    anti_aliasing=data.dtype.kind != "b")
             frame = data[f, :, :, :, :]
             if smooth > 0:
                 frame = scipy.median_filter(frame.astype(np.float32),

bioxelnodes/bioxelutils/common.py

@@ -259,11 +259,12 @@ def local_lib_not_updated():
     not_update = get_node_version() != addon_version
     return use_local and not_update
 
+
 def get_output_node(node_group):
     try:
         output_node = get_nodes_by_type(node_group,
                                         'NodeGroupOutput')[0]
     except:
         output_node = node_group.nodes.new("NodeGroupOutput")
-        
-    return output_node
+
+    return output_node

bioxelnodes/bioxelutils/node.py

@@ -1,13 +1,13 @@
 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 .common import get_file_prop, set_file_prop
+from ..exceptions import NoFound
 
 from ..constants import LATEST_NODE_LIB_PATH, VERSIONS
 
 
-def get_node_group(node_type: str, use_link=True):
+def get_node_tree(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
@@ -19,36 +19,37 @@ def get_node_group(node_type: str, use_link=True):
     if get_file_prop("node_version") is None:
         set_file_prop("node_version", addon_version)
 
-    local_lib_path = None
+    local_lib = None
     for node_group in bpy.data.node_groups:
         if node_group.name.startswith("BioxelNodes"):
             lib = node_group.library
             if lib:
                 lib_path = Path(bpy.path.abspath(lib.filepath)).resolve()
                 if lib_path != addon_lib_path:
-                    local_lib_path = lib_path
+                    local_lib = lib.filepath
                     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:
+    lib_path_str = local_lib or str(addon_lib_path)
+
+    with bpy.data.libraries.load(lib_path_str,
+                                 link=use_link,
+                                 relative=True) as (data_from, data_to):
+        data_to.node_groups = [n for n in data_from.node_groups
+                               if n == node_type]
+
+    node_tree = data_to.node_groups[0]
+
+    if node_tree is None:
         raise NoFound('No custom node found')
 
-    return node_group
+    return node_tree
 
 
-def assign_node_group(node, node_type: str):
-    node.node_tree = bpy.data.node_groups[node_type]
+def assign_node_tree(node, node_tree):
+    node.node_tree = node_tree
     node.width = 200.0
-    node.name = node_type
+    node.name = node_tree.name
     return node
 
 
@@ -61,9 +62,9 @@ def add_node_to_graph(node_name: str, node_group, node_label=None, use_link=True
         if node.select:
             node.select = False
 
-    get_node_group(node_type, use_link)
+    node_tree = get_node_tree(node_type, use_link)
     node = node_group.nodes.new("GeometryNodeGroup")
-    assign_node_group(node, node_type)
+    assign_node_tree(node, node_tree)
 
     node.label = node_label
     node.show_options = False

bioxelnodes/blender_manifest.toml

@@ -1,7 +1,7 @@
 schema_version = "1.0.0"
 
 id = "bioxelnodes"
-version = "1.0.1"
+version = "1.0.2"
 name = "Bioxel Nodes"
 tagline = "For scientific volumetric data visualization in Blender"
 maintainer = "Ma Nan <[email protected]>"

bioxelnodes/constants.py

@@ -1,6 +1,6 @@
 from pathlib import Path
 
-VERSIONS = [{"label": "Latest", "node_version": (1, 0, 1)},
+VERSIONS = [{"label": "Latest", "node_version": (1, 0, 2)},
             {"label": "v0.3.x", "node_version": (0, 3, 3)},
             {"label": "v0.2.x", "node_version": (0, 2, 9)}]
 

bioxelnodes/operators/container.py

@@ -343,7 +343,7 @@ def execute(self, context):
         if len(cut_nodes) == 0:
             cutter_node = add_node_to_graph("ObjectCutter",
                                             node_group,
-                                            node_label=name,
+                                            node_label=f"{self.cutter_type.capitalize()} Cutter",
                                             use_link=get_use_link())
             cutter_node.inputs[0].default_value = self.cutter_type.capitalize()
             cutter_node.inputs[1].default_value = cutter_obj

bioxelnodes/operators/io.py

@@ -164,7 +164,7 @@ class ParseVolumetricData(bpy.types.Operator):
     read_as: bpy.props.EnumProperty(name="Read as",
                                     default="SCALAR",
                                     items=[("SCALAR", "Scalar", ""),
-                                           ("LABEL", "Labels", ""),
+                                           ("LABEL", "Label", ""),
                                            ("COLOR", "Color", "")])  # type: ignore
 
     series_id: bpy.props.EnumProperty(name="Select Series",
@@ -284,6 +284,10 @@ def modal(self, context, event):
                 self.report({"ERROR"}, "Invaild label data.")
                 return {'CANCELLED'}
 
+            if self.label_count == 0:
+                self.report({"ERROR"}, "Get no label.")
+                return {'CANCELLED'}
+
         orig_shape = self.meta['xyz_shape']
         orig_spacing = self.meta['spacing']
 
@@ -418,8 +422,8 @@ def get_meta(key):
                     series_id = "empty"
 
                 label = "{:<20} {:>1}".format(f"{study_description}>{series_description}({series_modality})",
-                                                                f"({size_x}x{size_y})x{count}")
-                
+                                              f"({size_x}x{size_y})x{count}")
+
                 series_items[series_id] = label
 
             for series_id, label in series_items.items():
@@ -500,10 +504,13 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
 
     label_count: bpy.props.IntProperty()  # type: ignore
 
+    smooth: bpy.props.IntProperty(name="Smooth Size (Larger takes longer time)",
+                                  default=3)  # type: ignore
+
     read_as: bpy.props.EnumProperty(name="Read as",
                                     default="SCALAR",
                                     items=[("SCALAR", "Scalar", ""),
-                                           ("LABEL", "Labels", ""),
+                                           ("LABEL", "Label", ""),
                                            ("COLOR", "Color", "")])  # type: ignore
 
     bioxel_size: bpy.props.FloatProperty(name="Bioxel Size (Larger size means small resolution)",
@@ -616,12 +623,15 @@ def progress_callback(frame, total):
                     progress_callback = progress_callback_factory(name_i,
                                                                   progress,
                                                                   progress_step)
+                    label_data = data == np.full_like(data, i+1)
+                    label_data = label_data.astype(np.float32)
                     try:
-                        layer = Layer(data=data == np.full_like(data, i+1),
+                        layer = Layer(data=label_data,
                                       name=name_i,
                                       kind=kind)
 
                         layer.resize(shape=shape,
+                                     smooth=self.smooth,
                                      progress_callback=progress_callback)
 
                         layer.affine = affine
@@ -924,6 +934,8 @@ def draw(self, context):
         if self.read_as == "SCALAR":
             panel.prop(self, "split_channel",
                        text=f"Split Channel as Multi Layer")
+        elif self.read_as == "LABEL":
+            panel.prop(self, "smooth")
 
         panel.label(
             text="Dimension Order: [Frame, (X-axis,Y-axis,Z-axis), Channel]")

bioxelnodes/operators/layer.py

@@ -4,7 +4,6 @@
 import numpy as np
 
 
-
 from ..exceptions import NoContent
 from ..bioxel.layer import Layer
 from ..bioxelutils.node import add_node_to_graph
@@ -199,14 +198,24 @@ def invoke(self, context, event):
             return self.execute(context)
 
 
-class RelocateLayer(bpy.types.Operator, LayerOperator):
+class RelocateLayer(bpy.types.Operator):
     bl_idname = "bioxelnodes.relocate_layer"
     bl_label = "Relocate Layer Cache"
     bl_description = "Relocate layer cache"
     bl_icon = "FILE"
 
     filepath: bpy.props.StringProperty(subtype="FILE_PATH")  # type: ignore
 
+    def execute(self, context):
+        layer_obj = get_selected_layer(context)
+        if layer_obj == None:
+            self.report({"WARNING"}, "Get no layer.")
+            return {'FINISHED'}
+
+        self.operate(layer_obj, context)
+
+        return {'FINISHED'}
+
     def operate(self, layer_obj, context):
         layer_obj.data.filepath = self.filepath
 
@@ -259,7 +268,7 @@ class ResampleLayer(bpy.types.Operator, OutputLayerOperator):
     bl_description = "Resample value"
     bl_icon = "ALIASED"
 
-    smooth: bpy.props.IntProperty(name="Smooth Iteration",
+    smooth: bpy.props.IntProperty(name="Smooth Size",
                                   default=0,
                                   soft_min=0, soft_max=5,
                                   options={"SKIP_SAVE"})  # type: ignore
@@ -389,7 +398,7 @@ def operate(self, orig_layer: Layer, context):
             if self.invert else data > self.threshold
 
         new_layer = orig_layer.copy()
-        new_layer.fill(self.fill_value, mask, 3)
+        new_layer.fill(self.fill_value, mask, 0)
         new_layer.name = self.new_layer_name \
             or f"{orig_layer.name}_F-{self.threshold:.2f}"
         return new_layer
@@ -419,7 +428,7 @@ def operate(self, orig_layer: Layer, context):
             (data > self.from_min) & (data < self.from_max)
 
         new_layer = orig_layer.copy()
-        new_layer.fill(self.fill_value, mask, 3)
+        new_layer.fill(self.fill_value, mask, 0)
         new_layer.name = self.new_layer_name \
             or f"{orig_layer.name}_F-{self.from_min:.2f}-{self.from_max:.2f}"
         return new_layer
@@ -431,7 +440,7 @@ class FillByLabel(bpy.types.Operator, FillOperator):
     bl_description = "Fill value by label"
     bl_icon = "MESH_CAPSULE"
 
-    smooth: bpy.props.IntProperty(name="Smooth Iteration",
+    smooth: bpy.props.IntProperty(name="Smooth Size",
                                   default=0,
                                   soft_min=0, soft_max=5,
                                   options={"SKIP_SAVE"})  # type: ignore
@@ -451,7 +460,7 @@ def operate(self, orig_layer: Layer, context):
             mask = 1 - mask
 
         new_layer = orig_layer.copy()
-        new_layer.fill(self.fill_value, mask, 3)
+        new_layer.fill(self.fill_value, mask, 0)
         new_layer.name = self.new_layer_name \
             or f"{orig_layer.name}_F-{label_layer.name}"
         return new_layer

bioxelnodes/operators/node.py

@@ -1,7 +1,7 @@
 import bpy
 
 from ..bioxelutils.common import is_incompatible, local_lib_not_updated
-from ..bioxelutils.node import assign_node_group, get_node_group
+from ..bioxelutils.node import assign_node_tree, get_node_tree
 from ..utils import get_use_link
 
 
@@ -41,14 +41,14 @@ def execute(self, context):
                         "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())
+        node_tree = get_node_tree(self.node_type, get_use_link())
         bpy.ops.node.add_node(
             'INVOKE_DEFAULT',
             type='GeometryNodeGroup',
             use_transform=True
         )
         node = bpy.context.active_node
-        assign_node_group(node, self.node_type)
+        assign_node_tree(node, node_tree)
         node.label = self.node_label
 
         node.show_options = False

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "bioxelnodes"
-version = "1.0.1"
+version = "1.0.2"
 description = ""
 authors = ["Ma Nan <[email protected]>"]
 license = "MIT"