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feat: redesign nodes

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This commit is contained in:
马南
2024-05-29 11:00:38 +08:00
parent d380cf7036
commit fa031e63f8
16 changed files with 937 additions and 466 deletions
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19
README.md
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@@ -17,7 +17,7 @@ Below are some examples with Bioxel Nodes. Thanks to Cycles Render, the volumetr
![gallery](docs/assets/gallery.png)
The "Bioxel" in "BioxelNodes", is a combination of the words "Bio-" and "Voxel". Bioxel is a voxel that stores biological data. The volumetric data made up of Bioxel is called Bioxels. We are developing a toolkit around Bioxels for better biological data visualization. but before its release, we made this Blender version of bioxels toolkit first, in order to let more people to have fun with volumetric data. [Getting Started](https://omoolab.github.io/BioxelNodes/latest/getting-started)
The "Bioxel" in "Bioxel Nodes", is a combination of the words "Bio-" and "Voxel". Bioxel is a voxel that stores biological data. We are developing a toolkit around Bioxel for better biological data visualization. but before its release, we made this Blender version of bioxels toolkit first, in order to let more people to have fun with volumetric data. [Getting Started](https://omoolab.github.io/BioxelNodes/latest/getting-started)
# Supported Format
@@ -41,5 +41,18 @@ The "Bioxel" in "BioxelNodes", is a combination of the words "Bio-" and "Voxel".
# Known limitations
- Sections cannot be generated
- Time sequence volume not supported (will be supported soon)
- Sections cannot be generated (will be supported soon)
- Time sequence volume not supported (will be supported soon)
# To Upgrade Add-on
To upgrade from an older version of the add-on to the latest, you need to do the following:
1. Remove the old version of Bioxel Nodes at Preferences > Add-ons
2. Add the new version and restart Blender.
It is not support editing the same blender file across add-on versions. In order to make sure that the previous file works properly. You need to save the staged data before upgrading ( read the last section of [Getting Started](https://omoolab.github.io/BioxelNodes/latest/getting-started/#share-your-file) ).
But even then, there is still no guarantee that the new version of the add-on will work on the old blender file. Therefore, it is highly recommended to open a new blender file to start the creating, not based on the old one.
Alternatively, objects from the old file that have nothing to do with Bioxel Nodes could be append to the new blender file.

6
bioxelnodes/__init__.py
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@@ -9,7 +9,7 @@ bl_info = {
"author": "Ma Nan",
"description": "",
"blender": (4, 0, 0),
"version": (0, 1, 1),
"version": (0, 2, 0),
"location": "File -> Import",
"warning": "",
"category": "Node"
@@ -21,8 +21,8 @@ auto_load.init()
def register():
auto_load.register()
menus.add()
bpy.types.Scene.bioxels_dir = bpy.props.StringProperty(
name="Bioxels Directory",
bpy.types.Scene.bioxel_layer_dir = bpy.props.StringProperty(
name="Bioxel Layers Directory",
subtype='DIR_PATH',
default="//"
)

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bioxelnodes/assets/Nodes/BioxelNodes_4.0.blend LFS
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bioxelnodes/assets/Nodes/BioxelNodes_4.1.blend LFS
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57
bioxelnodes/convert.py
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@@ -1,57 +0,0 @@
import bpy
from .utils import get_bioxels_obj, get_node_by_type
class ConvertToMesh(bpy.types.Operator):
bl_idname = "bioxelnodes.convert_to_mesh"
bl_label = "Bioxels To Mesh"
bl_description = "Convert Bioxels To Mesh"
bl_options = {'UNDO'}
@classmethod
def poll(cls, context):
bioxels_obj = None
for obj in bpy.context.selected_objects:
bioxels_obj = get_bioxels_obj(obj)
break
return True if bioxels_obj else False
def execute(self, context):
bioxels_objs = []
for obj in bpy.context.selected_objects:
bioxels_obj = get_bioxels_obj(obj)
if bioxels_obj:
bioxels_objs.append(bioxels_obj)
if len(bioxels_objs) == 0:
self.report({"WARNING"}, "Cannot find any bioxels.")
return {'FINISHED'}
for bioxels_obj in bioxels_objs:
bpy.ops.mesh.primitive_cube_add(
size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
mesh_obj = bpy.context.active_object
mesh_obj.name = f"{bioxels_obj.parent.name}_Mesh"
bpy.ops.node.new_geometry_nodes_modifier()
modifier = mesh_obj.modifiers[0]
nodes = modifier.node_group.nodes
links = modifier.node_group.links
output_node = get_node_by_type(nodes, 'NodeGroupOutput')[0]
object_node = nodes.new("GeometryNodeObjectInfo")
realize_nodes = nodes.new("GeometryNodeRealizeInstances")
object_node.inputs[0].default_value = bioxels_obj
object_node.transform_space = 'RELATIVE'
links.new(object_node.outputs['Geometry'], realize_nodes.inputs[0])
links.new(realize_nodes.outputs[0], output_node.inputs[0])
bpy.ops.object.convert(target='MESH')
bpy.context.object.active_material_index = 1
bpy.ops.object.material_slot_remove()
self.report({"INFO"}, f"Successfully convert to mesh")
return {'FINISHED'}

7
bioxelnodes/customnodes/menus.py
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@@ -146,10 +146,13 @@ class CustomNodes():
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 != 'separator' else None
item_items = item.get('items')
if item_items:
self._find_item(found_items, item_items, node_type)
@@ -169,7 +172,7 @@ class CustomNodes():
op.node_callback = item.get('node_callback') or ""
return op.add_node(node_tree)
else:
raise RuntimeError("No custom node type found.")
raise RuntimeError("Not found in menu.")
def register(self):
for cls in self.menu_classes:

479
bioxelnodes/io.py
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@@ -6,16 +6,18 @@ import numpy as np
from pathlib import Path
from uuid import uuid4
import mathutils
import math
from .utils import calc_bbox_verts, get_text_index_str, get_bioxels_obj, get_node_by_type, show_message
from .nodes import custom_nodes
from .props import BIOXELNODES_Series
from .utils import (calc_bbox_verts, get_container, get_layer, get_text_index_str,
get_node_by_type, hide_in_ray, lock_transform, show_message)
try:
import SimpleITK as sitk
except:
...
SUPPORT_EXTS = ['.dcm', '.DICOM',
SUPPORT_EXTS = ['.dcm', '.DCM', '.DICOM',
'.bmp', '.BMP',
'.PIC', '.pic',
'.gipl', '.gipl.gz',
@@ -31,15 +33,15 @@ SUPPORT_EXTS = ['.dcm', '.DICOM',
'.png', '.PNG',
'.vtk']
SEQUENCE_EXTS = ['.dcm', '.DICOM',
SEQUENCE_EXTS = ['.dcm', '.DCM', '.DICOM',
'.bmp', '.BMP',
'.jpg', '.JPG', '.jpeg', '.JPEG',
'.tif', '.TIF', '.tiff', '.TIFF',
'.png', '.PNG']
DICOM_EXTS = ['.dcm', '.DICOM']
DICOM_EXTS = ['.dcm', '.DCM', '.DICOM']
FH_EXTS = ['.dcm', '.DICOM',
FH_EXTS = ['.dcm', '.DCM', '.DICOM',
'.gipl', '.gipl.gz',
'.mnc', '.MNC',
'.mrc', '.rec',
@@ -51,7 +53,7 @@ FH_EXTS = ['.dcm', '.DICOM',
'.gz']
def get_bioxels_shape(bioxel_size: float, orig_shape: tuple, orig_spacing: tuple):
def get_layer_shape(bioxel_size: float, orig_shape: tuple, orig_spacing: tuple):
shape = (int(orig_shape[0] / bioxel_size * orig_spacing[0]),
int(orig_shape[1] / bioxel_size * orig_spacing[1]),
int(orig_shape[2] / bioxel_size * orig_spacing[2]))
@@ -132,27 +134,31 @@ def read_image(filepath: str, series_id=""):
def rgb2gray(image):
# Convert sRGB image to gray scale and rescale results to [0,255]
channels = [sitk.VectorIndexSelectionCast(
layers = [sitk.VectorIndexSelectionCast(
image, i, sitk.sitkFloat32) for i in range(image.GetNumberOfComponentsPerPixel())]
# linear mapping
I = (0.2126*channels[0] + 0.7152*channels[1] + 0.0722*channels[2])
I = (0.2126*layers[0] + 0.7152*layers[1] + 0.0722*layers[2])
return sitk.Cast(I, sitk.sitkFloat32)
def x2gray(image):
return sitk.VectorIndexSelectionCast(image, 0, sitk.sitkUInt16)
class ImportVolumeDataDialog(bpy.types.Operator):
bl_idname = "bioxelnodes.import_volume_data_dialog"
bl_label = "Volume Data as Bioxels"
bl_description = "Import Volume Data as Bioxels (VDB)"
bl_label = "Volume Data as Bioxel Layer"
bl_description = "Import Volume Data as Bioxel Layer"
bl_options = {'UNDO'}
filepath: bpy.props.StringProperty(
subtype="FILE_PATH",
options={'HIDDEN'}
subtype="FILE_PATH"
) # type: ignore
container_name: bpy.props.StringProperty() # type: ignore
layer_name: bpy.props.StringProperty() # type: ignore
series_id: bpy.props.StringProperty() # type: ignore
resample_method: bpy.props.EnumProperty(
@@ -163,6 +169,8 @@ class ImportVolumeDataDialog(bpy.types.Operator):
("gaussian", "Gaussian", "")]
) # type: ignore
container: bpy.props.StringProperty() # type: ignore
read_as: bpy.props.EnumProperty(
name="Read as",
default="scalar",
@@ -170,15 +178,10 @@ class ImportVolumeDataDialog(bpy.types.Operator):
("labels", "Labels", "")]
) # type: ignore
label_index: bpy.props.IntProperty(
name="Label Index",
default=1
) # type: ignore
bioxel_size: bpy.props.FloatProperty(
name="Bioxel Size (Larger size means small resolution)",
soft_min=0.1, soft_max=10.0,
min=1e-2, max=1e2,
min=0.1, max=1e2,
default=1,
) # type: ignore
@@ -193,7 +196,7 @@ class ImportVolumeDataDialog(bpy.types.Operator):
) # type: ignore
scene_scale: bpy.props.FloatProperty(
name="Scene Scale (Bioxels Unit pre Blender Unit)",
name="Scene Scale (Bioxel Unit pre Blender Unit)",
soft_min=0.001, soft_max=100.0,
min=1e-6, max=1e6,
default=0.01,
@@ -210,20 +213,20 @@ class ImportVolumeDataDialog(bpy.types.Operator):
) # type: ignore
def execute(self, context):
image, bioxels_name = read_image(self.filepath, self.series_id)
image, name = read_image(self.filepath, self.series_id)
container_name = self.container_name or name
bioxel_size = self.bioxel_size
orig_spacing = self.orig_spacing
image_spacing = image.GetSpacing()
image_shape = image.GetSize()
bioxels_spacing = (
layer_spacing = (
image_spacing[0] / orig_spacing[0] * bioxel_size,
image_spacing[1] / orig_spacing[1] * bioxel_size,
image_spacing[2] / orig_spacing[2] * bioxel_size
)
bioxels_shape = get_bioxels_shape(
layer_shape = get_layer_shape(
bioxel_size, image_shape, orig_spacing)
if self.read_as == "labels":
@@ -254,11 +257,11 @@ class ImportVolumeDataDialog(bpy.types.Operator):
print(f"Resampling...")
image = sitk.Resample(
image1=image,
size=bioxels_shape,
size=layer_shape,
transform=sitk.Transform(),
interpolator=interpolator,
outputOrigin=image.GetOrigin(),
outputSpacing=bioxels_spacing,
outputSpacing=layer_spacing,
outputDirection=image.GetDirection(),
defaultPixelValue=default_value,
outputPixelType=image.GetPixelID(),
@@ -281,63 +284,15 @@ class ImportVolumeDataDialog(bpy.types.Operator):
# A (nterior) j -> j -> y
# S (uperior) k -> i -> z
array = sitk.GetArrayFromImage(image)
orig_dtype = str(array.dtype)
# print(f"Coverting Dtype from {orig_dtype} to float...")
# array = array.astype(float)
if array.ndim == 4:
# if array.shape[0] == 3 and self.read_as == "scalar":
# # RGB -> Grayscale
# array = np.dot(array[..., :3], [0.2989, 0.5870, 0.1140])
# else:
# array = array[:, :, :, 0]
array = array[:, :, :, 0]
array = np.transpose(array)
bioxels_shape = array.shape
bioxels_offset = 0.0
if self.read_as == "labels":
array = array == np.full_like(array, self.label_index)
bioxels_default_threshold = 1.0
bioxels_max = 1.0
bioxels_min = 0.0
bioxels_name = f"{bioxels_name}_{self.label_index}"
else:
if self.invert_scalar:
array = -array
orig_max = float(np.max(array))
orig_min = float(np.min(array))
orig_median = float(np.median(array))
orig_percentile80 = float(np.percentile(array, 80)) \
if self.invert_scalar else float(np.percentile(array, 80))
# if (orig_dtype[0] != "u" and orig_min < 0) \
# or (orig_dtype[0] == "u" and self.invert_scalar):
if orig_min < 0:
bioxels_offset = -orig_min
array = array + np.full_like(array, bioxels_offset)
bioxels_default_threshold = orig_percentile80
bioxels_max = float(np.max(array))
bioxels_min = float(np.min(array))
stats_table = [("Max", orig_max),
("Min", orig_min),
("Median", orig_median),
("80%", orig_percentile80)]
print("Bioxels Value Stats:")
for stats in stats_table:
print("| {: >10} | {: >40} |".format(*stats))
# # Build VDB
grid = vdb.BoolGrid() if self.read_as == "labels" else vdb.FloatGrid()
grid.copyFromArray(array.copy().astype(float))
# After sitk.DICOMOrient(), origin and direction will also orient base on LPS
# so we need to convert them into RAS
mat_lps2ras = axis_conversion(
@@ -365,139 +320,237 @@ class ImportVolumeDataDialog(bpy.types.Operator):
transfrom = mat_lps2ras @ mat_location @ mat_rotation @ mat_scale \
if self.do_orient else mat_location @ mat_rotation @ mat_scale
grid.transform = vdb.createLinearTransform(transfrom.transposed())
grid.name = "scalar"
# Wrapper a Container
if not self.container:
# Make transformation
scene_scale = float(self.scene_scale)
# (S)uperior -Z -> Y
# (A)osterior Y -> Z
mat_ras2blender = axis_conversion(
from_forward='-Z',
from_up='Y',
to_forward='Y',
to_up='Z'
).to_4x4()
mat_scene_scale = mathutils.Matrix.Scale(
scene_scale, 4
)
bpy.ops.mesh.primitive_cube_add(
enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1)
)
container = bpy.context.active_object
bbox_verts = calc_bbox_verts((0, 0, 0), array.shape)
for index, vert in enumerate(container.data.vertices):
bbox_transform = transfrom
vert.co = bbox_transform @ mathutils.Vector(bbox_verts[index])
container.matrix_world = mat_ras2blender @ mat_scene_scale
container.name = container_name
container.data.name = container_name
container['bioxel_container'] = True
container['scene_scale'] = scene_scale
bpy.ops.node.new_geometry_nodes_modifier()
container_node_tree = container.modifiers[0].node_group
input_node = get_node_by_type(container_node_tree.nodes,
'NodeGroupInput')[0]
container_node_tree.links.remove(input_node.outputs[0].links[0])
# bpy.ops.mesh.primitive_cube_add(
# enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1)
# )
# frame = bpy.context.active_object
# bbox_verts = calc_bbox_verts((0, 0, 0), array.shape)
# for index, vert in enumerate(frame.data.vertices):
# # bbox_transform = mat_ras2blender @ mat_scene_scale @ transfrom
# bbox_transform = transfrom
# vert.co = bbox_transform @ mathutils.Vector(bbox_verts[index])
# frame.name = f"Frame_{container_name}"
# frame.data.name = f"Frame_{container_name}"
# lock_transform(frame)
# hide_in_ray(frame)
# frame.hide_select = True
# frame.hide_render = True
# frame.display_type = 'WIRE'
# frame.parent = container
else:
container = bpy.data.objects[self.container]
container_node_tree = container.modifiers[0].node_group
preferences = context.preferences.addons[__package__].preferences
vdb_dirpath = Path(preferences.cache_dir, 'VDBs')
vdb_dirpath.mkdir(parents=True, exist_ok=True)
vdb_path = Path(vdb_dirpath, f"{uuid4()}.vdb")
cache_dir = Path(preferences.cache_dir, 'VDBs')
cache_dir.mkdir(parents=True, exist_ok=True)
print(f"Storing the VDB file ({str(vdb_path)})...")
vdb.write(str(vdb_path), grids=[grid])
loc, rot, sca = transfrom.decompose()
# Read VDB
print(f"Importing the VDB file to Blender scene...")
bpy.ops.object.volume_import(
filepath=str(vdb_path), align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
layer_origin = tuple(loc)
layer_rotation = tuple(rot.to_euler())
layer_shape = tuple(array.shape)
bioxels_obj = bpy.context.active_object
def create_layer(array, layer_name, layer_type="scalar"):
grid = vdb.FloatGrid()
array = array.copy().astype(float)
grid.copyFromArray(array)
grid.transform = vdb.createLinearTransform(transfrom.transposed())
grid.name = layer_type
# Set props to VDB object
bioxels_obj.name = f"{bioxels_name}_Bioxels"
bioxels_obj.data.name = f"{bioxels_name}_Bioxels"
vdb_path = Path(cache_dir, f"{uuid4()}.vdb")
print(f"Storing the cache ({str(vdb_path)})...")
vdb.write(str(vdb_path), grids=[grid])
# Make transformation
scene_scale = float(self.scene_scale)
# Read VDB
print(f"Loading the cache to Blender scene...")
bpy.ops.object.volume_import(
filepath=str(vdb_path), align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
# (S)uperior -Z -> Y
# (A)osterior Y -> Z
mat_ras2blender = axis_conversion(
from_forward='-Z',
from_up='Y',
to_forward='Y',
to_up='Z'
).to_4x4()
layer = bpy.context.active_object
mat_scene_scale = mathutils.Matrix.Scale(
scene_scale, 4
)
# Set props to VDB object
layer.name = layer_name
layer.data.name = layer_name
bioxels_obj.matrix_world = mat_ras2blender @ mat_scene_scale
bioxels_obj.lock_location[0] = True
bioxels_obj.lock_location[1] = True
bioxels_obj.lock_location[2] = True
bioxels_obj.lock_rotation[0] = True
bioxels_obj.lock_rotation[1] = True
bioxels_obj.lock_rotation[2] = True
bioxels_obj.lock_scale[0] = True
bioxels_obj.lock_scale[1] = True
bioxels_obj.lock_scale[2] = True
bioxels_obj.hide_select = True
bioxels_obj['bioxels'] = True
lock_transform(layer)
hide_in_ray(layer)
layer.hide_select = True
layer.hide_render = True
layer.hide_viewport = True
layer.data.display.use_slice = True
layer.data.display.density = 1e-05
bpy.ops.node.new_geometry_nodes_modifier()
node_tree = bioxels_obj.modifiers[0].node_group
layer['bioxel_layer'] = True
layer['bioxel_layer_type'] = layer_type
layer.parent = container
# Wrapper a Container
bpy.ops.mesh.primitive_cube_add(
enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1)
)
container_obj = bpy.context.active_object
bbox_verts = calc_bbox_verts((0, 0, 0), bioxels_shape)
for index, vert in enumerate(container_obj.data.vertices):
bbox_transform = mat_ras2blender @ mat_scene_scale @ transfrom
vert.co = bbox_transform @ mathutils.Vector(bbox_verts[index])
for collection in layer.users_collection:
collection.objects.unlink(layer)
bioxels_obj.parent = container_obj
container_obj.name = bioxels_name
container_obj.data.name = bioxels_name
container_obj.visible_camera = False
container_obj.visible_diffuse = False
container_obj.visible_glossy = False
container_obj.visible_transmission = False
container_obj.visible_volume_scatter = False
container_obj.visible_shadow = False
container_obj.display_type = 'WIRE'
container_obj['bioxels_container'] = True
container_obj['scene_scale'] = scene_scale
container_obj['bioxel_size'] = bioxel_size
container_obj['bioxels_max'] = bioxels_max
container_obj['bioxels_min'] = bioxels_min
container_obj['bioxels_offset'] = bioxels_offset
container_obj['bioxels_shape'] = bioxels_shape
for collection in container.users_collection:
collection.objects.link(layer)
bpy.ops.object.modifier_add(type='NODES')
container_obj.modifiers[0].node_group = node_tree
container_obj.modifiers[0].show_in_editmode = False
container_obj.modifiers[0].show_viewport = False
container_obj.modifiers[0].show_render = False
print(f"Creating layer ...")
# Create BioxelNodes to VDB object
print(f"Creating BioxelNodes to the VDB...")
if preferences.do_add_segmentnode:
bpy.ops.node.new_geometry_nodes_modifier()
node_tree = layer.modifiers[0].node_group
nodes = node_tree.nodes
links = node_tree.links
input_node = get_node_by_type(nodes, 'NodeGroupInput')[0]
output_node = get_node_by_type(nodes, 'NodeGroupOutput')[0]
segment_node = custom_nodes.add_node(
nodes, 'BioxelNodes_Segment')
node_type = 'BioxelNodes_AsLabel' if layer_type == "label" else 'BioxelNodes_AsScalar'
source_node = custom_nodes.add_node(nodes, node_type)
segment_node.inputs['Threshold'].default_value = bioxels_default_threshold
links.new(input_node.outputs[0], source_node.inputs[0])
links.new(source_node.outputs[0], output_node.inputs[0])
links.new(input_node.outputs[0], segment_node.inputs[0])
links.new(segment_node.outputs[0], output_node.inputs[0])
source_node.inputs['Bioxel Size'].default_value = bioxel_size
source_node.inputs['Shape'].default_value = layer_shape
source_node.inputs['Origin'].default_value = layer_origin
source_node.inputs['Rotation'].default_value = layer_rotation
return layer
if self.read_as == "labels":
orig_max = int(np.max(array))
orig_min = int(np.min(array))
layer_name = self.layer_name or "Label"
for i in range(orig_max):
label = array == np.full_like(array, i+1)
layer = create_layer(array=label,
layer_name=f"{container_name}_{layer_name}_{i+1}",
layer_type="label")
output_node = get_node_by_type(container_node_tree.nodes,
'NodeGroupOutput')[0]
mask_node = custom_nodes.add_node(container_node_tree.nodes,
'BioxelNodes_MaskByLabel')
mask_node.inputs[0].default_value = layer
if len(output_node.inputs[0].links) == 0:
container_node_tree.links.new(mask_node.outputs[0],
output_node.inputs[0])
else:
if self.invert_scalar:
array = -array
orig_max = float(np.max(array))
orig_min = float(np.min(array))
orig_median = float(np.median(array))
orig_percentile80 = float(np.percentile(array, 80)) \
if self.invert_scalar else float(np.percentile(array, 80))
stats_table = [("Max", orig_max),
("Min", orig_min),
("Median", orig_median),
("80%", orig_percentile80)]
print("Volume Data Stats:")
for stats in stats_table:
print("| {: >10} | {: >40} |".format(*stats))
scalar_offset = 0
if orig_min < 0:
scalar_offset = -orig_min
array = array + np.full_like(array, scalar_offset)
layer_name = self.layer_name or "Scalar"
layer = create_layer(array=array,
layer_name=f"{container_name}_{layer_name}",
layer_type="scalar")
layer_node_tree = layer.modifiers[0].node_group
source_node = layer_node_tree.nodes['BioxelNodes_AsScalar']
source_node.inputs['Offset'].default_value = scalar_offset
source_node.inputs['Max'].default_value = orig_max
source_node.inputs['Min'].default_value = orig_min
output_node = get_node_by_type(container_node_tree.nodes,
'NodeGroupOutput')[0]
mask_node = custom_nodes.add_node(container_node_tree.nodes,
'BioxelNodes_MaskByThreshold')
mask_node.inputs[0].default_value = layer
if len(output_node.inputs[0].links) == 0:
container_node_tree.links.new(mask_node.outputs[0],
output_node.inputs[0])
bpy.context.view_layer.objects.active = container
# Change render setting for better result
if preferences.do_change_render_setting:
bpy.context.scene.render.engine = 'CYCLES'
bpy.context.scene.cycles.volume_bounces = 12
bpy.context.scene.cycles.transparent_max_bounces = 64
bpy.context.scene.cycles.transparent_max_bounces = 16
bpy.context.scene.cycles.volume_preview_step_rate = 10
self.report({"INFO"}, "Successfully Imported")
return {'FINISHED'}
def invoke(self, context, event):
min_size = min(
self.orig_spacing[0], self.orig_spacing[1], self.orig_spacing[2])
default_size = 1.0
self.bioxel_size = min_size if min_size > default_size else default_size
context.window_manager.invoke_props_dialog(self, width=400)
return {'RUNNING_MODAL'}
def draw(self, context):
layout = self.layout
bioxels_shape = get_bioxels_shape(
layer_shape = get_layer_shape(
self.bioxel_size, self.orig_shape, self.orig_spacing)
bioxel_count = bioxels_shape[0] * bioxels_shape[1] * bioxels_shape[2]
text = f"Shape will be: {str(bioxels_shape)} {bioxel_count:,} "
bioxel_count = layer_shape[0] * layer_shape[1] * layer_shape[2]
text = f"Shape will be: {str(layer_shape)} {bioxel_count:,} "
if bioxel_count > 100000000:
text += "**TOO LARGE!**"
layout = self.layout
panel = layout.box()
panel.prop(self, "container_name")
panel.prop(self, "layer_name")
panel = layout.box()
panel.prop(self, "resample_method")
panel.prop(self, "bioxel_size")
@@ -505,16 +558,18 @@ class ImportVolumeDataDialog(bpy.types.Operator):
row.prop(self, "orig_spacing")
panel.label(text=text)
panel = layout.box()
panel.prop(self, "do_orient")
panel = layout.box()
panel.prop(self, "read_as")
if self.read_as == "labels":
panel.prop(self, "label_index")
...
else:
panel.prop(self, "invert_scalar")
panel = layout.box()
panel.prop(self, "scene_scale")
panel.prop(self, "do_orient")
def get_series_ids(self, context):
@@ -530,14 +585,15 @@ def get_series_ids(self, context):
return items
class ReadDICOM(bpy.types.Operator):
bl_idname = "bioxelnodes.read_dicom"
bl_label = "Volume Data as Bioxels"
bl_description = "Import Volume Data as Bioxels (VDB)"
class ParseVolumeData(bpy.types.Operator):
bl_idname = "bioxelnodes.parse_volume_data"
bl_label = "Volume Data as Bioxel Layer"
bl_description = "Import Volume Data as Bioxel Layer"
bl_options = {'UNDO'}
filepath: bpy.props.StringProperty(subtype="FILE_PATH") # type: ignore
directory: bpy.props.StringProperty(subtype='DIR_PATH') # type: ignore
container: bpy.props.StringProperty() # type: ignore
series_id: bpy.props.EnumProperty(
name="Select Series",
@@ -555,25 +611,41 @@ class ReadDICOM(bpy.types.Operator):
print("Collecting Meta Data...")
image, name = read_image(self.filepath, self.series_id)
stats_table = [("Shape", str(image.GetSize())),
("Spacing", str(image.GetSpacing())),
("Origin", str(image.GetOrigin())),
("Direction", str(image.GetDirection())),
("Data Type", image.GetPixelIDTypeAsString())]
for k in image.GetMetaDataKeys():
stats_table.append((k, str(image.GetMetaData(k))))
print("Meta Data:")
for stats in stats_table:
print("| {: >10} | {: >40} |".format(*stats))
print("| {: >20} | {: >100} |".format(*stats))
do_orient = ext not in SEQUENCE_EXTS or ext in DICOM_EXTS
orig_shape = image.GetSize()
orig_spacing = image.GetSpacing()
min_size = min(orig_spacing[0], orig_spacing[1], orig_spacing[2])
bioxel_size = max(min_size, 1.0)
if self.container:
container = bpy.data.objects[self.container]
container_name = container.name
else:
container_name = name
bpy.ops.bioxelnodes.import_volume_data_dialog(
'INVOKE_DEFAULT',
filepath=self.filepath,
orig_shape=image.GetSize(),
orig_spacing=image.GetSpacing(),
container_name=container_name,
orig_shape=orig_shape,
orig_spacing=orig_spacing,
bioxel_size=bioxel_size,
series_id=self.series_id or "",
do_orient=do_orient
do_orient=do_orient,
container=self.container
)
self.report({"INFO"}, "Successfully Readed.")
@@ -623,15 +695,15 @@ class ReadDICOM(bpy.types.Operator):
class ImportVolumeData(bpy.types.Operator):
bl_idname = "bioxelnodes.import_volume_data"
bl_label = "Volume Data as Bioxels"
bl_description = "Import Volume Data as Bioxels (VDB)"
bl_label = "Volume Data as Bioxel Layer"
bl_description = "Import Volume Data as Bioxel Layer"
bl_options = {'UNDO'}
filepath: bpy.props.StringProperty(subtype="FILE_PATH") # type: ignore
directory: bpy.props.StringProperty(subtype='DIR_PATH') # type: ignore
def execute(self, context):
bpy.ops.bioxelnodes.read_dicom(
bpy.ops.bioxelnodes.parse_volume_data(
'INVOKE_DEFAULT',
filepath=self.filepath,
directory=self.directory
@@ -647,7 +719,7 @@ try:
class BIOXELNODES_FH_ImportVolumeData(bpy.types.FileHandler):
bl_idname = "BIOXELNODES_FH_ImportVolumeData"
bl_label = "File handler for dicom import"
bl_import_operator = "bioxelnodes.read_dicom"
bl_import_operator = "bioxelnodes.parse_volume_data"
bl_file_extensions = ";".join(FH_EXTS)
@classmethod
@@ -657,10 +729,40 @@ except:
...
class AddVolumeData(bpy.types.Operator):
bl_idname = "bioxelnodes.add_volume_data"
bl_label = "Add Volume Data to Container"
bl_description = "Add Volume Data to Container"
bl_options = {'UNDO'}
filepath: bpy.props.StringProperty(subtype="FILE_PATH") # type: ignore
directory: bpy.props.StringProperty(subtype='DIR_PATH') # type: ignore
@classmethod
def poll(cls, context):
container = get_container(bpy.context.active_object)
return True if container else False
def execute(self, context):
container = get_container(bpy.context.active_object)
bpy.ops.bioxelnodes.parse_volume_data(
'INVOKE_DEFAULT',
filepath=self.filepath,
directory=self.directory,
container=container.name
)
return {'FINISHED'}
def invoke(self, context, event):
context.window_manager.fileselect_add(self)
return {'RUNNING_MODAL'}
class ExportVDB(bpy.types.Operator):
bl_idname = "bioxelnodes.export_vdb"
bl_label = "Bioxels as VDB"
bl_description = "Export Bioxels original VDB data"
bl_label = "Bioxel Layer as VDB"
bl_description = "Export Bioxel Layer as VDB"
bl_options = {'UNDO'}
filepath: bpy.props.StringProperty(
@@ -671,26 +773,19 @@ class ExportVDB(bpy.types.Operator):
@classmethod
def poll(cls, context):
bioxels_obj = None
for obj in bpy.context.selected_objects:
bioxels_obj = get_bioxels_obj(obj)
break
return True if bioxels_obj else False
layer = get_layer(bpy.context.active_object)
return True if layer else False
def invoke(self, context, event):
context.window_manager.fileselect_add(self)
return {'RUNNING_MODAL'}
def execute(self, context):
bioxels_obj = None
for obj in bpy.context.selected_objects:
bioxels_obj = get_bioxels_obj(obj)
break
layer = get_layer(bpy.context.active_object)
filepath = f"{self.filepath.split('.')[0]}.vdb"
# "//"
source_dir = bpy.path.abspath(bioxels_obj.data.filepath)
source_dir = bpy.path.abspath(layer.data.filepath)
output_path: Path = Path(filepath).resolve()
source_path: Path = Path(source_dir).resolve()

38
bioxelnodes/menus.py
View File

@@ -1,18 +1,32 @@
import bpy
from .convert import ConvertToMesh
from .io import ExportVDB, ImportVolumeData
from .misc import SaveBioxels
from .operators import ConvertToMesh, JoinLayers
from .io import ExportVDB, ImportVolumeData, AddVolumeData
from .misc import SaveBioxelLayers
class ObjectMenu(bpy.types.Menu):
bl_idname = "BIOXELNODES_MT_OBJECT"
bl_label = "Bioxels"
class View3DBioxelsMenu(bpy.types.Menu):
bl_idname = "BIOXELNODES_MT_VIEW3D"
bl_label = "Bioxel Nodes"
def draw(self, context):
layout = self.layout
layout.operator(ConvertToMesh.bl_idname)
layout.operator(AddVolumeData.bl_idname)
layout.separator()
layout.operator(SaveBioxels.bl_idname)
layout.operator(SaveBioxelLayers.bl_idname)
class OutlinerBioxelsMenu(bpy.types.Menu):
bl_idname = "BIOXELNODES_MT_OUTLINER"
bl_label = "Bioxel Nodes"
def draw(self, context):
layout = self.layout
layout.operator(JoinLayers.bl_idname)
layout.operator(ConvertToMesh.bl_idname)
layout.operator(AddVolumeData.bl_idname)
layout.separator()
layout.operator(SaveBioxelLayers.bl_idname)
def TOPBAR_FILE_IMPORT(self, context):
@@ -29,17 +43,25 @@ def TOPBAR_FILE_EXPORT(self, context):
def VIEW3D_OBJECT(self, context):
layout = self.layout
layout.menu(ObjectMenu.bl_idname)
layout.menu(View3DBioxelsMenu.bl_idname)
layout.separator()
def OUTLINER_OBJECT(self, context):
layout = self.layout
layout.menu(OutlinerBioxelsMenu.bl_idname)
layout.separator()
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.prepend(OUTLINER_OBJECT)
bpy.types.VIEW3D_MT_object_context_menu.prepend(VIEW3D_OBJECT)
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)

115
bioxelnodes/misc.py
View File

@@ -1,97 +1,86 @@
import bpy
from pathlib import Path
import shutil
from bioxelnodes.utils import get_all_bioxels_objs, get_bioxels_obj
from bioxelnodes.utils import get_all_layers, get_container, get_container_layers
class SaveBioxels(bpy.types.Operator):
bl_idname = "bioxelnodes.save_bioxels"
bl_label = "Save Bioxels"
bl_description = "Save Bioxels to Directory."
def save_layer(layer, output_dir):
name = layer.name
# "//"
output_dir = bpy.path.abspath(output_dir)
source_dir = bpy.path.abspath(layer.data.filepath)
output_path: Path = Path(output_dir, f"{name}.vdb").resolve()
source_path: Path = Path(source_dir).resolve()
if output_path != source_path:
shutil.copy(source_path, output_path)
blend_path = Path(bpy.path.abspath("//")).resolve()
layer.data.filepath = bpy.path.relpath(
str(output_path), start=str(blend_path))
class SaveBioxelLayers(bpy.types.Operator):
bl_idname = "bioxelnodes.save_bioxel_layers"
bl_label = "Save Bioxel Layers"
bl_description = "Save Bioxel Layers to Directory."
bl_options = {'UNDO'}
@classmethod
def poll(cls, context):
bioxels_obj = None
for obj in bpy.context.selected_objects:
bioxels_obj = get_bioxels_obj(obj)
break
return True if bioxels_obj else False
container = get_container(bpy.context.active_object)
return True if container else False
def execute(self, context):
bioxels_objs = []
container = get_container(bpy.context.active_object)
for obj in bpy.context.selected_objects:
bioxels_obj = get_bioxels_obj(obj)
if bioxels_obj:
bioxels_objs.append(bioxels_obj)
if len(bioxels_objs) == 0:
self.report({"WARNING"}, "Cannot find any bioxels.")
if not container:
self.report({"WARNING"}, "Cannot find any bioxel container.")
return {'FINISHED'}
for bioxels_obj in bioxels_objs:
name = bioxels_obj.parent.name
for layer in get_container_layers(container):
try:
save_layer(layer, context.scene.bioxel_layer_dir)
except:
self.report(
{"WARNING"}, f"Fail to save {layer.name}, skiped")
# "//"
bioxels_dir = bpy.path.abspath(context.scene.bioxels_dir)
source_dir = bpy.path.abspath(bioxels_obj.data.filepath)
output_path: Path = Path(bioxels_dir, f"{name}.vdb").resolve()
source_path: Path = Path(source_dir).resolve()
if output_path != source_path:
shutil.copy(source_path, output_path)
blend_path = Path(bpy.path.abspath("//")).resolve()
bioxels_obj.data.filepath = bpy.path.relpath(
str(output_path), start=str(blend_path))
self.report({"INFO"}, f"Successfully saved bioxels")
self.report({"INFO"}, f"Successfully saved bioxel layers.")
return {'FINISHED'}
class SaveAllBioxels(bpy.types.Operator):
bl_idname = "bioxelnodes.save_all_bioxels"
bl_label = "Save All Bioxels"
bl_description = "Save All Bioxels to Directory."
class SaveAllBioxelLayers(bpy.types.Operator):
bl_idname = "bioxelnodes.save_all_bioxel_layers"
bl_label = "Save All Bioxel Layers"
bl_description = "Save All Bioxel Layers to Directory."
bl_options = {'UNDO'}
def execute(self, context):
bioxels_objs = get_all_bioxels_objs()
layers = get_all_layers()
if len(bioxels_objs) == 0:
self.report({"WARNING"}, "Cannot find any bioxels.")
if len(layers) == 0:
self.report({"WARNING"}, "Cannot find any bioxel layer.")
return {'FINISHED'}
for bioxels_obj in bioxels_objs:
name = bioxels_obj.parent.name
for layer in layers:
try:
save_layer(layer, context.scene.bioxel_layer_dir)
except:
self.report(
{"WARNING"}, f"Fail to save {layer.name}, skiped")
# "//"
bioxels_dir = bpy.path.abspath(context.scene.bioxels_dir)
source_dir = bpy.path.abspath(bioxels_obj.data.filepath)
output_path: Path = Path(bioxels_dir, f"{name}.vdb").resolve()
source_path: Path = Path(source_dir).resolve()
if output_path != source_path:
shutil.copy(source_path, output_path)
blend_path = Path(bpy.path.abspath("//")).resolve()
bioxels_obj.data.filepath = bpy.path.relpath(
str(output_path), start=str(blend_path))
self.report({"INFO"}, f"Successfully saved bioxels")
self.report({"INFO"}, f"Successfully saved bioxel layers.")
return {'FINISHED'}
class BIOXELNODES_PT_Bioxels(bpy.types.Panel):
bl_idname = "BIOXELNODES_PT_Bioxels"
bl_label = "Bioxels"
bl_label = "Bioxel Nodes"
bl_space_type = "PROPERTIES"
bl_region_type = "WINDOW"
bl_context = "scene"
@@ -99,5 +88,5 @@ class BIOXELNODES_PT_Bioxels(bpy.types.Panel):
def draw(self, context):
layout = self.layout
scene = context.scene
layout.prop(scene, 'bioxels_dir')
layout.operator(SaveAllBioxels.bl_idname)
layout.prop(scene, 'bioxel_layer_dir')
layout.operator(SaveAllBioxelLayers.bl_idname)

405
bioxelnodes/nodes.py
View File

@@ -38,112 +38,311 @@ else:
return callback_str
MENU_ITEMS = [
{
'label': 'Presets',
'icon': 'MESH_MONKEY',
'items': [
{
'label': 'Segment',
'icon': 'BONE_DATA',
'node_type': 'BioxelNodes_Segment',
'node_description': '',
'node_callback': "\n".join([
set_prop_to_node_factory("bioxel_size", "Detail Size"),
set_prop_to_node_factory("bioxels_offset", "Offset"),
])
}
# {
# 'label': 'Anatomy',
# 'icon': 'CONSTRAINT_BONE',
# 'node_type': 'BioxelNodes_Anatomy',
# 'node_description': '',
# 'node_callback': "\n".join([
# set_prop_to_node_factory("bioxel_size", "Detail Size"),
# set_prop_to_node_factory("bioxels_offset", "Offset"),
# ])
# }
]
},
{
'label': 'Segment',
'icon': 'OUTLINER_DATA_VOLUME',
'items': [
{
'label': 'Segment by Level',
'icon': 'EMPTY_SINGLE_ARROW',
'node_type': 'BioxelNodes_SegmentByLevel',
'node_description': '',
'node_callback': "\n".join([
set_prop_to_node_factory("bioxel_size", "Detail Size"),
set_prop_to_node_factory("bioxels_offset", "Offset"),
])
},
{
'label': 'Segment by Range',
'icon': 'IPO_CONSTANT',
'node_type': 'BioxelNodes_SegmentByRange',
'node_description': '',
'node_callback': "\n".join([
set_prop_to_node_factory("bioxel_size", "Detail Size"),
set_prop_to_node_factory("bioxels_offset", "Offset"),
])
}
# {
# 'label': 'Segment by Layers',
# 'icon': 'ALIGN_JUSTIFY',
# 'node_type': 'BioxelNodes_SegmentsByLayers',
# 'node_description': '',
# 'node_callback': "\n".join([
# set_prop_to_node_factory("bioxel_size", "Detail Size"),
# set_prop_to_node_factory("bioxels_offset", "Offset"),
# ])
# }
]
},
{
'label': 'Shader',
'icon': 'SHADING_RENDERED',
'items': [
{
'label': 'Segment Shader',
'icon': 'OUTLINER_OB_VOLUME',
'node_type': 'BioxelNodes_SegmentShader',
'node_description': ''
}
]
}
]
NODE_FILE = "BioxelNodes_4.0"
if bpy.app.version >= (4, 1, 0):
MENU_ITEMS.append({
'label': 'Slicer',
'icon': 'CLIPUV_DEHLT',
'items': [
{
'label': 'RAS Slicer',
'icon': 'EMPTY_DATA',
'node_type': 'BioxelNodes_RAS-Slicer',
'node_description': ''
},
{
'label': 'Axis Slicer',
'icon': 'OUTLINER_OB_EMPTY',
'node_type': 'BioxelNodes_AxisSlicer',
'node_description': '',
},
{
'label': 'Box Slicer',
'icon': 'MOD_WIREFRAME',
'node_type': 'BioxelNodes_BoxSlicer',
'node_description': '',
}
]
})
NODE_FILE = "BioxelNodes_4.1"
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': 'Solid Shader',
'icon': 'SHADING_SOLID',
'node_type': 'BioxelNodes_AssignSolidShader',
'node_description': ''
},
{
'label': 'Slime Shader',
'icon': 'OUTLINER_OB_META',
'node_type': 'BioxelNodes_AssignSlimeShader',
'node_description': ''
},
{
'label': 'Volume Shader',
'icon': 'OUTLINER_OB_VOLUME',
'node_type': 'BioxelNodes_AssignVolumeShader',
'node_description': ''
},
{
'label': 'Universal Shader',
'icon': 'SHADING_RENDERED',
'node_type': 'BioxelNodes_AssignUniversalShader',
'node_description': ''
}
]
},
{
'label': 'Colors',
'icon': 'COLOR',
'items': [
{
'label': 'Color Presets',
'icon': 'COLOR',
'node_type': 'BioxelNodes_SetColorPresets',
'node_description': ''
},
{
'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': 'Slicers',
'icon': 'MOD_BEVEL',
'items': [
{
'label': 'Apply Slicers',
'icon': 'MOD_BEVEL',
'node_type': 'BioxelNodes_ApplySlicers',
'node_description': ''
},
"separator",
{
'label': 'Plane Slicer',
'icon': 'MOD_LATTICE',
'node_type': 'BioxelNodes_PlaneSlicer',
'node_description': '',
},
{
'label': 'Object Plane Slicer',
'icon': 'OUTLINER_OB_LATTICE',
'node_type': 'BioxelNodes_ObjectPlaneSlicer',
'node_description': '',
}
]
},
{
'label': 'Utils',
'icon': 'MODIFIER',
'items': [
{
'label': 'Join Component',
'icon': 'CONSTRAINT_BONE',
'node_type': 'BioxelNodes_JoinComponent',
'node_description': ''
},
{
'label': 'Separate Component',
'node_type': 'BioxelNodes_SeparateComponent',
'node_description': ''
}
]
},
{
'label': 'Others',
'icon': 'PACKAGE',
'items': [
{
'label': 'Source As Label',
'icon': 'GP_SELECT_POINTS',
'node_type': 'BioxelNodes_AsLabel',
'node_description': ''
},
{
'label': 'Source As Scalar',
'icon': 'GP_SELECT_STROKES',
'node_type': 'BioxelNodes_AsScalar',
'node_description': ''
}
]
}
]
else:
NODE_FILE = "BioxelNodes_4.0"
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': 'Solid Shader',
'icon': 'SHADING_SOLID',
'node_type': 'BioxelNodes_AssignSolidShader',
'node_description': ''
},
{
'label': 'Slime Shader',
'icon': 'OUTLINER_OB_META',
'node_type': 'BioxelNodes_AssignSlimeShader',
'node_description': ''
},
{
'label': 'Volume Shader',
'icon': 'OUTLINER_OB_VOLUME',
'node_type': 'BioxelNodes_AssignVolumeShader',
'node_description': ''
},
{
'label': 'Universal Shader',
'icon': 'SHADING_RENDERED',
'node_type': 'BioxelNodes_AssignUniversalShader',
'node_description': ''
}
]
},
{
'label': 'Colors',
'icon': 'COLOR',
'items': [
{
'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': 'Slicers',
'icon': 'MOD_BEVEL',
'items': [
{
'label': 'Apply Slicers',
'icon': 'MOD_BEVEL',
'node_type': 'BioxelNodes_ApplySlicers',
'node_description': ''
},
"separator",
{
'label': 'Plane Slicer',
'icon': 'MOD_LATTICE',
'node_type': 'BioxelNodes_PlaneSlicer',
'node_description': '',
},
{
'label': 'Object Plane Slicer',
'icon': 'OUTLINER_OB_LATTICE',
'node_type': 'BioxelNodes_ObjectPlaneSlicer',
'node_description': '',
}
]
},
{
'label': 'Utils',
'icon': 'MODIFIER',
'items': [
{
'label': 'Join Component',
'icon': 'CONSTRAINT_BONE',
'node_type': 'BioxelNodes_JoinComponent',
'node_description': ''
},
{
'label': 'Separate Component',
'node_type': 'BioxelNodes_SeparateComponent',
'node_description': ''
}
]
},
{
'label': 'Others',
'icon': 'PACKAGE',
'items': [
{
'label': 'Source As Label',
'icon': 'GP_SELECT_POINTS',
'node_type': 'BioxelNodes_AsLabel',
'node_description': ''
},
{
'label': 'Source As Scalar',
'icon': 'GP_SELECT_STROKES',
'node_type': 'BioxelNodes_AsScalar',
'node_description': ''
}
]
}
]
custom_nodes = CustomNodes(
menu_items=MENU_ITEMS,

188
bioxelnodes/operators.py Normal file
View File

@@ -0,0 +1,188 @@
from pathlib import Path
import bpy
import pyopenvdb as vdb
from uuid import uuid4
from .nodes import custom_nodes
from .utils import (get_container, get_container_layers,
get_layer, get_node_by_type, hide_in_ray, lock_transform)
def get_scalar_layer_selection(self, context):
items = [("None", "None", "")]
base_layer = bpy.data.objects[self.base_layer]
container = base_layer.parent
for layer in get_container_layers(container):
if layer.get("bioxel_layer_type") == "scalar":
items.append((
layer.name,
layer.name,
""
))
return items
def get_label_layer_selection(self, context):
items = [("None", "None", "")]
base_layer = bpy.data.objects[self.base_layer]
container = base_layer.parent
for layer in get_container_layers(container):
if layer.get("bioxel_layer_type") == "label":
items.append((
layer.name,
layer.name,
""
))
return items
class JoinLayers(bpy.types.Operator):
bl_idname = "bioxelnodes.join_layers"
bl_label = "Join Additinal Layers"
bl_description = "Join Layers"
bl_options = {'UNDO'}
base_layer: bpy.props.StringProperty(
options={"HIDDEN"}
) # type: ignore
scalar_layer: bpy.props.EnumProperty(
name="Scaler Layer",
items=get_scalar_layer_selection
) # type: ignore
label_layer: bpy.props.EnumProperty(
name="Label Layer",
items=get_label_layer_selection
) # type: ignore
# color_layer: bpy.props.StringProperty() # type: ignore
@classmethod
def poll(cls, context):
layer = get_layer(bpy.context.active_object)
return True if layer else False
def execute(self, context):
base_layer = bpy.data.objects[self.base_layer]
if not base_layer:
self.report({"WARNING"}, "Cannot find any bioxel layer as base.")
return {'FINISHED'}
base_layer_dir = bpy.path.abspath(base_layer.data.filepath)
base_grids, base_metadata = vdb.readAll(base_layer_dir)
preferences = context.preferences.addons[__package__].preferences
cache_dir = Path(preferences.cache_dir, 'VDBs')
cache_dir.mkdir(parents=True, exist_ok=True)
layers = []
if self.scalar_layer != "None":
layers.append(bpy.data.objects[self.scalar_layer])
if self.label_layer != "None":
layers.append(bpy.data.objects[self.label_layer])
# if self.color_layer:
# layers.append(bpy.data.objects[self.color_layer])
if len(layers) == 0:
self.report({"WARNING"}, "No additinal layers setted.")
return {'FINISHED'}
for layer in layers:
layer_dir = bpy.path.abspath(layer.data.filepath)
grids, metadata = vdb.readAll(layer_dir)
base_grids.extend(grids)
vdb_path = Path(cache_dir, f"{uuid4()}.vdb")
print(f"Storing the VDB file ({str(vdb_path)})...")
vdb.write(str(vdb_path), grids=base_grids)
# Read VDB
print(f"Loading the cache to Blender scene...")
bpy.ops.object.volume_import(
filepath=str(vdb_path), align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
joined_layer = bpy.context.active_object
bpy.ops.object.modifier_add(type='NODES')
joined_layer.modifiers[0].node_group = base_layer.modifiers[0].node_group
# Set props to VDB object
joined_layer.name = f"{base_layer.name}_Joined"
joined_layer.data.name = f"{base_layer.name}_Joined"
lock_transform(joined_layer)
hide_in_ray(joined_layer)
joined_layer.hide_select = True
joined_layer.hide_render = True
joined_layer.hide_viewport = True
joined_layer.data.display.use_slice = True
joined_layer.data.display.density = 1e-05
joined_layer['bioxel_layer'] = True
joined_layer.parent = base_layer.parent
return {'FINISHED'}
def invoke(self, context, event):
base_layer = get_layer(bpy.context.active_object)
self.base_layer = base_layer.name
context.window_manager.invoke_props_dialog(self, width=400)
return {'RUNNING_MODAL'}
class ConvertToMesh(bpy.types.Operator):
bl_idname = "bioxelnodes.convert_to_mesh"
bl_label = "Bioxel Components To Mesh"
bl_description = "Convert Bioxel Components To Mesh"
bl_options = {'UNDO'}
@classmethod
def poll(cls, context):
container = get_container(bpy.context.active_object)
return True if container else False
def execute(self, context):
container = get_container(bpy.context.active_object)
if not container:
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))
mesh = bpy.context.active_object
mesh.name = f"Mesh_{container.name}"
bpy.ops.object.constraint_add(type='COPY_TRANSFORMS')
mesh.constraints["Copy Transforms"].target = container
bpy.ops.node.new_geometry_nodes_modifier()
modifier = mesh.modifiers[0]
nodes = modifier.node_group.nodes
links = modifier.node_group.links
output_node = get_node_by_type(nodes, 'NodeGroupOutput')[0]
object_node = nodes.new("GeometryNodeObjectInfo")
realize_nodes = nodes.new("GeometryNodeRealizeInstances")
separate_node = custom_nodes.add_node(
nodes, "BioxelNodes_SeparateComponent")
object_node.inputs[0].default_value = container
separate_node.inputs[1].default_value = 1
links.new(object_node.outputs['Geometry'], separate_node.inputs[0])
links.new(separate_node.outputs[0], realize_nodes.inputs[0])
links.new(realize_nodes.outputs[0], output_node.inputs[0])
bpy.ops.object.convert(target='MESH')
bpy.ops.constraint.apply(constraint="Copy Transforms", owner='OBJECT')
bpy.context.object.active_material_index = 1
bpy.ops.object.material_slot_remove()
self.report({"INFO"}, f"Successfully convert to mesh")
return {'FINISHED'}

6
bioxelnodes/preferences.py
View File

@@ -12,11 +12,6 @@ class BioxelNodesPreferences(bpy.types.AddonPreferences, ExternalPackagePreferen
default=str(Path(Path.home(), '.bioxelnodes'))
) # type: ignore
do_add_segmentnode: bpy.props.BoolProperty(
name="Add Segment Node",
default=True,
) # type: ignore
do_change_render_setting: bpy.props.BoolProperty(
name="Change Render Setting",
default=True,
@@ -33,4 +28,3 @@ class BioxelNodesPreferences(bpy.types.AddonPreferences, ExternalPackagePreferen
layout.prop(self, 'cache_dir')
layout.prop(self, "do_change_render_setting")
layout.prop(self, "do_add_segmentnode")

69
bioxelnodes/utils.py
View File

@@ -9,6 +9,7 @@ def get_type(cls):
def get_node_by_type(nodes, type_name: str):
return [node for node in nodes if get_type(node) == type_name]
def show_message(message="", title="Message Box", icon='INFO'):
def draw(self, context):
@@ -67,33 +68,57 @@ def calc_bbox_verts(origin, size):
return bbox_verts
def get_bioxels_obj(current_obj):
bioxels_obj = None
if current_obj.get('bioxels_container'):
bioxels_values = []
for obj in bpy.data.objects:
if obj.parent == current_obj and obj.get('bioxels'):
bioxels_values.append(obj)
if len(bioxels_values) > 0:
bioxels_obj = bioxels_values[0]
elif current_obj.get('bioxels') and current_obj.parent:
if current_obj.parent.get('bioxels_container'):
bioxels_obj = current_obj
return bioxels_obj
def lock_transform(obj):
obj.lock_location[0] = True
obj.lock_location[1] = True
obj.lock_location[2] = True
obj.lock_rotation[0] = True
obj.lock_rotation[1] = True
obj.lock_rotation[2] = True
obj.lock_scale[0] = True
obj.lock_scale[1] = True
obj.lock_scale[2] = True
def get_all_bioxels_objs():
bioxels_objs = []
def hide_in_ray(obj):
obj.visible_camera = False
obj.visible_diffuse = False
obj.visible_glossy = False
obj.visible_transmission = False
obj.visible_volume_scatter = False
obj.visible_shadow = False
def get_container(current_obj):
if current_obj:
return current_obj if current_obj.get('bioxel_container') else None
else:
return None
def get_layer(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_layers(container):
layers = []
for obj in bpy.data.objects:
if obj.parent:
if obj.parent.get('bioxels_container') and obj.get('bioxels'):
bioxels_objs.append(obj)
if obj.parent == container and get_layer(obj):
layers.append(obj)
return list(set(bioxels_objs))
return layers
def get_all_layers():
layers = []
for obj in bpy.data.objects:
if get_layer(obj):
layers.append(obj)
return layers
def get_text_index_str(text):

2
docs/getting-started.md
View File

@@ -60,4 +60,4 @@ The VDB cache and the Bioxel nodes are not reachable to computers if you don't s
![before sharin](assets/before-sharing.png)
After that, both the VDB cache and the Bioxel nodes are stored in relative locations. When you share a file with someone, pack the entire directory so that the resources are not lost. The other person will be able to load correctly, regardless of whether they have BioxelNodes installed.
After that, both the VDB cache and the Bioxel nodes are stored in relative locations. When you share a file with someone, pack the entire directory so that the resources are not lost. The other person will be able to load correctly, regardless of whether they have Bioxel Nodes installed.

2
docs/index.md
View File

@@ -17,7 +17,7 @@ Below are some examples with Bioxel Nodes. Thanks to Cycles Render, the volumetr
![gallery](assets/gallery.png)
The "Bioxel" in "BioxelNodes", is a combination of the words "Bio-" and "Voxel". Bioxel is a voxel that stores biological data. The volumetric data made up of Bioxel is called Bioxels. We are developing a toolkit around Bioxels for better biological data visualization. but before its release, we made this Blender version of bioxels toolkit first, in order to let more people to have fun with volumetric data. [Getting Started](https://omoolab.github.io/BioxelNodes/latest/getting-started)
The "Bioxel" in "Bioxel Nodes", is a combination of the words "Bio-" and "Voxel". Bioxel is a voxel that stores biological data. The volumetric data made up of Bioxel is called Bioxels. We are developing a toolkit around Bioxels for better biological data visualization. but before its release, we made this Blender version of bioxels toolkit first, in order to let more people to have fun with volumetric data. [Getting Started](https://omoolab.github.io/BioxelNodes/latest/getting-started)
# Supported Format

2
pyproject.toml
View File

@@ -1,6 +1,6 @@
[tool.poetry]
name = "bioxelnodes"
version = "0.1.1"
version = "0.2.0"
description = ""
authors = ["Ma Nan <icrdr2010@outlook.com>"]
license = "MIT"