feat: layer list system

.gitignore

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

bioxelnodes/__init__.py

@@ -1,5 +1,6 @@
 import bpy
 
+from .props import BIOXELNODES_LayerListUL
 from . import auto_load
 from . import menus
 
@@ -9,11 +10,17 @@
 
 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

@@ -7,7 +7,6 @@
 
 # 3rd-party
 import transforms3d
-
 # TODO: turn to dataclasses
 
 
@@ -105,13 +104,13 @@ def resize(self, shape: tuple, progress_callback=None):
         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):
@@ -125,8 +124,10 @@ def resize(self, shape: tuple, progress_callback=None):
 
             factors = np.divide(self.shape, shape)
             zoom_factors = [1 / f for f in factors]
-            frame = ndi.zoom(data[f, :, :, :],
-                             zoom_factors,
+            frame = ndi.zoom(data[f, :, :, :, :],
+                             zoom_factors+[1.0],
+                             mode="nearest",
+                             grid_mode=False,
                              order=order)
 
             data_frames += (frame,)
@@ -137,7 +138,10 @@ def resize(self, shape: tuple, progress_callback=None):
         #     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

@@ -42,7 +42,8 @@
 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 +65,40 @@ 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
@@ -84,29 +107,42 @@ 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):
     file_dict = {}
     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
@@ -124,6 +160,12 @@ def collect_sequence(filepath: Path):
     return sequence
 
 
+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) -> Layer:
     """Parse any volumetric data to numpy with shap (T,X,Y,Z,C)
 
@@ -139,7 +181,7 @@ 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 +223,7 @@ 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 +287,7 @@ 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 +339,10 @@ def get_meta(key):
 
         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/container.py

@@ -5,9 +5,12 @@
 from mathutils import Matrix, Vector
 
 
-from .layer import Layer, get_container_layer_objs, layer_to_obj, obj_to_layer
+from .layer import Layer, layer_to_obj, obj_to_layer
 from ..nodes import custom_nodes
-from .node import get_nodes_by_type, move_node_to_node
+from .utils import (get_container_layer_objs,
+                    get_layer_prop_value,
+                    get_nodes_by_type,
+                    move_node_to_node)
 
 
 NODE_TYPE = {
@@ -66,59 +69,39 @@ 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 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]
+    container = Container(name=container_obj.name,
+                          layers=layers)
+    return container
 
 
 def add_layers(layers: list[Layer],
                container_obj: bpy.types.Object,
                cache_dir: str):
 
-    container_node_group = container_obj.modifiers[0].node_group
+    node_group = container_obj.modifiers[0].node_group
+    output_node = get_nodes_by_type(node_group,
+                                    'NodeGroupOutput')[0]
 
     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]
+        fetch_node = custom_nodes.add_node(node_group,
+                                           "BioxelNodes_FetchLayer")
+        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:
-            container_node_group.links.new(mask_node.outputs[0],
-                                           output_node.inputs[0])
-            move_node_to_node(mask_node, output_node, (-300, 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(mask_node, output_node, (0, -100 * (i+1)))
+            move_node_to_node(fetch_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]
-    container = Container(name=container_obj.name,
-                          layers=layers)
-    return container
-
-
 def container_to_obj(container: Container,
                      scene_scale: float,
                      cache_dir: str):
@@ -153,28 +136,16 @@ def container_to_obj(container: Container,
     container_obj.show_in_front = True
     container_obj['bioxel_container'] = True
 
-    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])
-
-    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)))
+    modifier = container_obj.modifiers.new("GeometryNodes", 'NODES')
+    node_group = bpy.data.node_groups.new('GeometryNodes', 'GeometryNodeTree')
+    node_group.interface.new_socket(name="Component",
+                                    in_out="OUTPUT",
+                                    socket_type="NodeSocketGeometry")
+    modifier.node_group = node_group
+    node_group.nodes.new("NodeGroupOutput")
+
+    container_obj = add_layers(container.layers,
+                               container_obj=container_obj,
+                               cache_dir=cache_dir)
 
     return container_obj