Merge pull request #44 from OmooLab/feature/dev

Feature/dev

bioxelnodes/bioxel/parse.py

@@ -61,7 +61,8 @@ def get_ext(filepath: Path) -> str:
     elif filepath.name.endswith(".map.gz"):
         return ".map.gz"
     else:
-        return filepath.suffix
+        suffix = filepath.suffix
+        return "" if len(suffix) > 5 else suffix
 
 
 def get_filename(filepath: Path):
@@ -310,6 +311,7 @@ def parse_volumetric_data(data_file: str, series_id="", progress_callback=None):
             def get_meta(key):
                 try:
                     stirng = reader.GetMetaData(0, key).removesuffix(" ")
+                    stirng.encode('utf-8')
                     if stirng in ["No study description",
                                   "No series description",
                                   ""]:

bioxelnodes/bioxelutils/common.py

@@ -2,7 +2,7 @@ from ast import literal_eval
 from pathlib import Path
 import bpy
 
-from ..constants import NODE_LIB_DIRPATH, VERSIONS
+from ..constants import LATEST_NODE_LIB_PATH, NODE_LIB_DIRPATH, VERSIONS
 from ..utils import get_cache_dir
 
 
@@ -244,7 +244,7 @@ def get_node_lib_path(node_version):
 
 def local_lib_not_updated():
     addon_version = VERSIONS[0]["node_version"]
-    addon_lib_path = get_node_lib_path(addon_version)
+    addon_lib_path = LATEST_NODE_LIB_PATH
 
     use_local = False
     for node_group in bpy.data.node_groups:
@@ -258,3 +258,12 @@ 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

bioxelnodes/bioxelutils/container.py

@@ -8,7 +8,7 @@ from mathutils import Matrix, Vector
 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,
+                     get_nodes_by_type, get_output_node,
                      move_node_to_node)
 from .node import add_node_to_graph
 from ..utils import get_use_link
@@ -82,11 +82,7 @@ def add_layers(layers: list[Layer],
                cache_dir: str):
 
     node_group = container_obj.modifiers[0].node_group
-    try:
-        output_node = get_nodes_by_type(node_group,
-                                        'NodeGroupOutput')[0]
-    except:
-        output_node = node_group.nodes.new("NodeGroupOutput")
+    output_node = get_output_node(node_group)
 
     for i, layer in enumerate(layers):
         layer_obj = layer_to_obj(layer, container_obj, cache_dir)

bioxelnodes/bioxelutils/node.py

@@ -4,7 +4,7 @@ import bpy
 from .common import get_file_prop, get_node_lib_path, set_file_prop
 from ..exceptions import Incompatible, NoFound
 
-from ..constants import VERSIONS
+from ..constants import LATEST_NODE_LIB_PATH, VERSIONS
 
 
 def get_node_group(node_type: str, use_link=True):
@@ -14,7 +14,7 @@ def get_node_group(node_type: str, use_link=True):
 
     # added node is always from latest node version
     addon_version = VERSIONS[0]["node_version"]
-    addon_lib_path = get_node_lib_path(addon_version)
+    addon_lib_path = LATEST_NODE_LIB_PATH
 
     if get_file_prop("node_version") is None:
         set_file_prop("node_version", addon_version)

bioxelnodes/blender_manifest.toml

@@ -1,7 +1,7 @@
 schema_version = "1.0.0"
 
 id = "bioxelnodes"
-version = "1.0.0"
+version = "1.0.1"
 name = "Bioxel Nodes"
 tagline = "For scientific volumetric data visualization in Blender"
 maintainer = "Ma Nan <icrdr2010@outlook.com>"
@@ -10,7 +10,7 @@ website = "https://omoolab.github.io/BioxelNodes/latest"
 
 tags = ["Geometry Nodes", "Render", "Import-Export"]
 blender_version_min = "4.2.0"
-license = ["SPDX:MIT"]
+license = ['SPDX:GPL-3.0-or-later']
 copyright = ["2024 OmooLab"]
 platforms = ["windows-x64", "linux-x64", "macos-arm64", "macos-x64"]
 

bioxelnodes/constants.py

@@ -1,12 +1,31 @@
 from pathlib import Path
 
-VERSIONS = [{"label": "Current", "node_version": (1, 0, 0)},
+VERSIONS = [{"label": "Latest", "node_version": (1, 0, 1)},
             {"label": "v0.3.x", "node_version": (0, 3, 3)},
             {"label": "v0.2.x", "node_version": (0, 2, 9)}]
 
 NODE_LIB_DIRPATH = Path(Path(__file__).parent,
                         "assets/Nodes").resolve()
 
+LATEST_NODE_LIB_PATH = lib_path = Path(NODE_LIB_DIRPATH,
+                                  "BioxelNodes_latest.blend").resolve()
+
+COMPONENT_OUTPUT_NODES = [
+    "CutoutByThreshold",
+    "CutoutByRange",
+    "CutoutByHue",
+    "JoinComponent",
+    "SetProperties",
+    "SetColor",
+    "SetColorByColor",
+    "SetColorByColor",
+    "SetColorByRamp2",
+    "SetColorByRamp3",
+    "SetColorByRamp4",
+    "SetColorByRamp5",
+    "Cut",
+]
+
 MENU_ITEMS = [
     {
         'label': 'Component',
@@ -179,9 +198,9 @@ MENU_ITEMS = [
         'icon': 'MODIFIER',
         'items': [
             {
-                'label': 'Fetch Surface',
+                'label': 'Fetch Mesh',
                 'icon': 'OUTLINER_OB_MESH',
-                'name': 'FetchSurface',
+                'name': 'FetchMesh',
                 'description': ''
             },
             {

bioxelnodes/menus.py

@@ -10,16 +10,19 @@ from .operators.layer import (FetchLayer, RelocateLayer, RetimeLayer, RenameLaye
                               RemoveSelectedLayers, SaveSelectedLayersCache,
                               ResampleLayer, SignScalar, CombineLabels,
                               FillByLabel, FillByThreshold, FillByRange)
-from .operators.container import (AddLocator, AddSlicer, ExtractShapeWire,
+from .operators.container import (AddLocator, AddSlicer, ContainerProps,
                                   SaveContainerLayersCache, RemoveContainerMissingLayers,
                                   SaveContainer, LoadContainer,
                                   AddPieCutter, AddPlaneCutter,
                                   AddCylinderCutter, AddCubeCutter, AddSphereCutter,
-                                  ExtractBboxWire, ExtractSurface, ExtractVolume, ContainerProps)
+                                  ExtractBboxWire, ExtractMesh, ExtractShapeWire,
+                                  ExtractNodeMesh, ExtractNodeBboxWire, ExtractNodeShapeWire)
 
 from .operators.io import (ImportAsLabel, ImportAsScalar, ImportAsColor)
 from .operators.misc import (CleanTemp,
-                             ReLinkNodeLib, RemoveAllMissingLayers, RenderSettingPreset, SaveAllLayersCache, SaveNodeLib, SliceViewer)
+                             ReLinkNodeLib, RemoveAllMissingLayers,
+                             RenderSettingPreset, SaveAllLayersCache,
+                             SaveNodeLib, SliceViewer)
 
 
 class IncompatibleMenu(bpy.types.Menu):
@@ -76,8 +79,7 @@ class ExtractFromContainerMenu(bpy.types.Menu):
 
     def draw(self, context):
         layout = self.layout
-        layout.operator(ExtractSurface.bl_idname)
-        layout.operator(ExtractVolume.bl_idname)
+        layout.operator(ExtractMesh.bl_idname)
         layout.operator(ExtractShapeWire.bl_idname)
         layout.operator(ExtractBboxWire.bl_idname)
 
@@ -199,8 +201,8 @@ class BioxelNodesTopbarMenu(bpy.types.Menu):
         layout.operator(RemoveAllMissingLayers.bl_idname)
 
         layout.separator()
-        layout.operator(SaveNodeLib.bl_idname)
         layout.menu(ReLinkNodeLibMenu.bl_idname)
+        layout.operator(SaveNodeLib.bl_idname)
 
         layout.separator()
         layout.menu(DangerZoneMenu.bl_idname)
@@ -257,6 +259,11 @@ class NodeContextMenu(bpy.types.Menu):
 
     def draw(self, context):
         layout = self.layout
+        layout.operator(ExtractNodeMesh.bl_idname)
+        layout.operator(ExtractNodeShapeWire.bl_idname)
+        layout.operator(ExtractNodeBboxWire.bl_idname)
+
+        layout.separator()
         layout.operator(SaveSelectedLayersCache.bl_idname,
                         icon=SaveSelectedLayersCache.bl_icon)
         layout.operator(RemoveSelectedLayers.bl_idname)

bioxelnodes/operators/container.py

@@ -1,13 +1,15 @@
 import bpy
 
+
 import bmesh
 
+from ..constants import COMPONENT_OUTPUT_NODES
 from ..utils import get_cache_dir, get_use_link, select_object
 from ..bioxel.io import load_container, save_container
 from ..bioxelutils.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,
+from ..bioxelutils.common import (get_container_layer_objs, get_container_obj, get_node_type,
+                                  get_nodes_by_type, get_output_node, is_missing_layer,
                                   move_node_between_nodes,
                                   move_node_to_node,
                                   get_all_layer_objs)
@@ -77,7 +79,7 @@ class LoadContainer(bpy.types.Operator):
         return {'RUNNING_MODAL'}
 
 
-class ExtractObject():
+class ExtractNodeObject():
     bl_options = {'UNDO'}
 
     def execute(self, context):
@@ -87,6 +89,26 @@ class ExtractObject():
             self.report({"WARNING"}, "Cannot find any bioxel container.")
             return {'FINISHED'}
 
+        # nodes = [node for node in context.selected_nodes
+        #          if get_node_type(node).removeprefix("BioxelNodes_") in COMPONENT_OUTPUT_NODES]
+
+        if len(context.selected_nodes) == 0:
+            self.report({"WARNING"}, "No node selected.")
+            return {'FINISHED'}
+
+        selected_node = context.selected_nodes[0]
+        container_node_group = container_obj.modifiers[0].node_group
+
+        container_output_node = get_output_node(container_node_group)
+
+        if len(container_output_node.inputs[0].links) == 0:
+            pre_socket = None
+        else:
+            pre_socket = container_output_node.inputs[0].links[0].from_socket
+
+        container_node_group.links.new(selected_node.outputs[0],
+                                       container_output_node.inputs[0])
+
         bpy.ops.mesh.primitive_cube_add(
             size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
         obj = bpy.context.active_object
@@ -106,6 +128,15 @@ class ExtractObject():
         fetch_mesh_node.inputs[0].default_value = container_obj
         node_group.links.new(fetch_mesh_node.outputs[0], output_node.inputs[0])
 
+        for modifier in obj.modifiers:
+            bpy.ops.object.modifier_apply(modifier=modifier.name)
+
+        obj.data.materials.clear()
+
+        if pre_socket:
+            container_node_group.links.new(pre_socket,
+                                           container_output_node.inputs[0])
+
         select_object(obj)
 
         self.report({"INFO"}, f"Successfully picked")
@@ -113,24 +144,92 @@ class ExtractObject():
         return {'FINISHED'}
 
 
-class ExtractSurface(bpy.types.Operator, ExtractObject):
-    bl_idname = "bioxelnodes.fetch_mesh"
-    bl_label = "Extract Surface"
-    bl_description = "Extract Surface"
+class ExtractNodeMesh(bpy.types.Operator, ExtractNodeObject):
+    bl_idname = "bioxelnodes.extract_node_mesh"
+    bl_label = "Extract Mesh"
+    bl_description = "Extract Mesh"
     bl_icon = "OUTLINER_OB_MESH"
-    object_type = "Surface"
+    object_type = "Mesh"
 
 
-class ExtractVolume(bpy.types.Operator, ExtractObject):
-    bl_idname = "bioxelnodes.pick_volume"
-    bl_label = "Extract Volume"
-    bl_description = "Extract Volume"
-    bl_icon = "OUTLINER_OB_VOLUME"
-    object_type = "Volume"
+class ExtractNodeShapeWire(bpy.types.Operator, ExtractNodeObject):
+    bl_idname = "bioxelnodes.extract_node_shape_wire"
+    bl_label = "Extract Shape Wire"
+    bl_description = "Extract Shape Wire"
+    bl_icon = "FILE_VOLUME"
+    object_type = "ShapeWire"
+
+
+class ExtractNodeBboxWire(bpy.types.Operator, ExtractNodeObject):
+    bl_idname = "bioxelnodes.extract_node_bbox_wire"
+    bl_label = "Extract Bbox Wire"
+    bl_description = "Extract Bbox Wire"
+    bl_icon = "MESH_CUBE"
+    object_type = "BboxWire"
+
+
+class ExtractObject():
+    bl_options = {'UNDO'}
+
+    def execute(self, context):
+        container_obj = get_container_obj(context.object)
+
+        if container_obj is None:
+            self.report({"WARNING"}, "Cannot find any bioxel container.")
+            return {'FINISHED'}
+
+        bpy.ops.mesh.primitive_cube_add(
+            size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
+        obj = bpy.context.active_object
+
+        obj.name = f"{container_obj.name}_{self.object_type}"
+
+        bpy.ops.node.new_geometry_nodes_modifier()
+        modifier = obj.modifiers[0]
+        node_group = modifier.node_group
+
+        output_node = get_output_node(node_group)
+
+        fetch_mesh_node = add_node_to_graph(f"Fetch{self.object_type}",
+                                            node_group,
+                                            node_label=f"Fetch {self.object_type}",
+                                            use_link=get_use_link())
+
+        fetch_mesh_node.inputs[0].default_value = container_obj
+
+        if self.object_type == "Mesh":
+            node_group.links.new(
+                fetch_mesh_node.outputs[0], output_node.inputs[0])
+        else:
+            curve_to_mesh_node = node_group.nodes.new(
+                "GeometryNodeCurveToMesh")
+            node_group.links.new(
+                fetch_mesh_node.outputs[0], curve_to_mesh_node.inputs[0])
+            node_group.links.new(
+                curve_to_mesh_node.outputs[0], output_node.inputs[0])
+
+        for modifier in obj.modifiers:
+            bpy.ops.object.modifier_apply(modifier=modifier.name)
+
+        obj.data.materials.clear()
+
+        select_object(obj)
+
+        self.report({"INFO"}, f"Successfully picked")
+
+        return {'FINISHED'}
+
+
+class ExtractMesh(bpy.types.Operator, ExtractObject):
+    bl_idname = "bioxelnodes.extract_mesh"
+    bl_label = "Extract Mesh"
+    bl_description = "Extract Mesh"
+    bl_icon = "OUTLINER_OB_MESH"
+    object_type = "Mesh"
 
 
 class ExtractShapeWire(bpy.types.Operator, ExtractObject):
-    bl_idname = "bioxelnodes.pick_shape_wire"
+    bl_idname = "bioxelnodes.extract_shape_wire"
     bl_label = "Extract Shape Wire"
     bl_description = "Extract Shape Wire"
     bl_icon = "FILE_VOLUME"
@@ -138,7 +237,7 @@ class ExtractShapeWire(bpy.types.Operator, ExtractObject):
 
 
 class ExtractBboxWire(bpy.types.Operator, ExtractObject):
-    bl_idname = "bioxelnodes.pick_bbox_wire"
+    bl_idname = "bioxelnodes.extract_bbox_wire"
     bl_label = "Extract Bbox Wire"
     bl_description = "Extract Bbox Wire"
     bl_icon = "MESH_CUBE"
@@ -253,8 +352,8 @@ class AddCutter():
                                          node_group,
                                          use_link=get_use_link())
 
-            output_node = get_nodes_by_type(node_group,
-                                            'NodeGroupOutput')[0]
+            output_node = get_output_node(node_group)
+
             if len(output_node.inputs[0].links) == 0:
                 node_group.links.new(cut_node.outputs[0],
                                      output_node.inputs[0])
@@ -277,7 +376,7 @@ class AddCutter():
                                          node_name="ObjectCutter",
                                          node_label=name)
             node = bpy.context.active_node
-            node.inputs[0].default_value = name
+            node.inputs[0].default_value = self.cutter_type.capitalize()
             node.inputs[1].default_value = cutter_obj
 
         return {'FINISHED'}
@@ -368,8 +467,8 @@ class AddSlicer(bpy.types.Operator):
 
         slice_node.inputs[1].default_value = slicer_obj
 
-        output_node = get_nodes_by_type(node_group,
-                                        'NodeGroupOutput')[0]
+        output_node = get_output_node(node_group)
+
         if len(output_node.inputs[0].links) == 0:
             node_group.links.new(slice_node.outputs[0],
                                  output_node.inputs[0])
@@ -419,8 +518,8 @@ class AddLocator(bpy.types.Operator):
 
         parent_node.inputs[1].default_value = locator_obj
 
-        output_node = get_nodes_by_type(node_group,
-                                        'NodeGroupOutput')[0]
+        output_node = get_output_node(node_group)
+
         if len(output_node.inputs[0].links) == 0:
             node_group.links.new(parent_node.outputs[0],
                                  output_node.inputs[0])

bioxelnodes/operators/io.py

@@ -391,6 +391,7 @@ class ParseVolumetricData(bpy.types.Operator):
                 def get_meta(key):
                     try:
                         stirng = single.GetMetaData(key).removesuffix(" ")
+                        stirng.encode('utf-8')
                         if stirng in ["No study description",
                                       "No series description",
                                       ""]:
@@ -416,13 +417,15 @@ class ParseVolumetricData(bpy.types.Operator):
                 if series_id == "":
                     series_id = "empty"
 
-                series_items[series_id] = "{:<20} {:>1}".format(f"{study_description}>{series_description}({series_modality})",
+                label = "{:<20} {:>1}".format(f"{study_description}>{series_description}({series_modality})",
                                                                 f"({size_x}x{size_y})x{count}")
+                
+                series_items[series_id] = label
 
-            for key, value in series_items.items():
+            for series_id, label in series_items.items():
                 series_item = self.series_ids.add()
-                series_item.id = key
-                series_item.label = value
+                series_item.id = series_id
+                series_item.label = label
 
             if len(series_items.keys()) > 1:
                 self.skip_series_select = False

bioxelnodes/operators/misc.py

@@ -5,7 +5,7 @@ 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 ..constants import NODE_LIB_DIRPATH, VERSIONS
+from ..constants import LATEST_NODE_LIB_PATH, VERSIONS
 from ..utils import get_cache_dir
 
 
@@ -19,7 +19,8 @@ class ReLinkNodeLib(bpy.types.Operator):
 
     def execute(self, context):
         node_version = VERSIONS[self.index]['node_version']
-        lib_path = get_node_lib_path(node_version)
+        lib_path = get_node_lib_path(node_version) \
+            if self.index != 0 else LATEST_NODE_LIB_PATH
 
         node_libs = []
         for node_group in bpy.data.node_groups:
@@ -56,16 +57,23 @@ class SaveNodeLib(bpy.types.Operator):
 
     def execute(self, context):
         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"]
-                
-        lib_path = get_node_lib_path(node_version)
-        
+
+        if node_version == VERSIONS[0]["node_version"]:
+            lib_path = LATEST_NODE_LIB_PATH
+        else:
+            lib_path = get_node_lib_path(node_version)
+
+        version_str = "v"+".".join([str(i) for i in list(node_version)])
+
         lib_dir = bpy.path.abspath(self.lib_dir)
-        local_lib_path: Path = Path(lib_dir, lib_path.name).resolve()
+        local_lib_path: Path = Path(lib_dir,
+                                    f"BioxelNodes_{version_str}.blend").resolve()
         node_lib_path: Path = lib_path
         blend_path = Path(bpy.path.abspath("//")).resolve()
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "bioxelnodes"
-version = "1.0.0"
+version = "1.0.1"
 description = ""
 authors = ["Ma Nan <icrdr2010@outlook.com>"]
 license = "MIT"