704 lines
23 KiB
Python
704 lines
23 KiB
Python
import bpy
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import shutil
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from bpy_extras.io_utils import axis_conversion
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import pyopenvdb as vdb
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import numpy as np
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from pathlib import Path
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from uuid import uuid4
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import mathutils
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import math
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from .utils import calc_bbox_verts, get_text_index_str, get_bioxels_obj, get_node_by_type, show_message
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from .nodes import custom_nodes
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from .props import BIOXELNODES_Series
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try:
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import SimpleITK as sitk
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except:
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...
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SUPPORT_EXTS = ['.dcm', '.DICOM',
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'.bmp', '.BMP',
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'.PIC', '.pic',
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'.gipl', '.gipl.gz',
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'.jpg', '.JPG', '.jpeg', '.JPEG',
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'.lsm', '.LSM',
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'.tif', '.TIF', '.tiff', '.TIFF',
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'.mnc', '.MNC',
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'.mrc', '.rec',
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'.mha', '.mhd',
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'.hdf', '.h4', '.hdf4', '.he2', '.h5', '.hdf5', '.he5',
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'.nia', '.nii', '.nii.gz', '.hdr', '.img', '.img.gz',
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'.nrrd', '.nhdr',
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'.png', '.PNG',
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'.vtk']
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SEQUENCE_EXTS = ['.dcm', '.DICOM',
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'.bmp', '.BMP',
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'.jpg', '.JPG', '.jpeg', '.JPEG',
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'.tif', '.TIF', '.tiff', '.TIFF',
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'.png', '.PNG']
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DICOM_EXTS = ['.dcm', '.DICOM']
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FH_EXTS = ['.dcm', '.DICOM',
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'.gipl', '.gipl.gz',
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'.mnc', '.MNC',
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'.mrc', '.rec',
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'.mha', '.mhd',
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'.nia', '.nii', '.nii.gz', '.hdr', '.img', '.img.gz',
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'.hdf', '.h4', '.hdf4', '.he2', '.h5', '.hdf5', '.he5',
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'.nrrd', '.nhdr',
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'.vtk',
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'.gz']
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def get_bioxels_shape(bioxel_size: float, orig_shape: tuple, orig_spacing: tuple):
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shape = (int(orig_shape[0] / bioxel_size * orig_spacing[0]),
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int(orig_shape[1] / bioxel_size * orig_spacing[1]),
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int(orig_shape[2] / bioxel_size * orig_spacing[2]))
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return (shape[0] if shape[0] > 0 else 1,
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shape[1] if shape[1] > 0 else 1,
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shape[2] if shape[2] > 0 else 1)
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def get_ext(filepath: str) -> str:
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file_path = Path(filepath)
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if file_path.name.endswith(".nii.gz"):
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return ".nii.gz"
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elif file_path.name.endswith(".img.gz"):
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return ".img.gz"
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elif file_path.name.endswith(".gipl.gz"):
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return ".gipl.gz"
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else:
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return file_path.suffix
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def get_sequence_name(filepath: str) -> str:
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ext = get_ext(filepath)
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filename = Path(filepath).name.removesuffix(ext)
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index: str = get_text_index_str(filename)
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return filename.removesuffix(index)
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def get_sequence_index(filepath: str) -> int:
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ext = get_ext(filepath)
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filename = Path(filepath).name.removesuffix(ext)
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index: str = get_text_index_str(filename)
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return int(index) if index else 0
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def collect_image_sequence(filepath: str):
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file_path = Path(filepath).resolve()
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files = list(file_path.parent.iterdir())
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files = [f for f in files if f.is_file()
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and get_ext(file_path) == get_ext(f)
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and get_sequence_name(file_path) == get_sequence_name(f)]
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files.sort(key=get_sequence_index)
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sequence = [str(f) for f in files]
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return sequence
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def read_image(filepath: str, series_id=""):
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ext = get_ext(filepath)
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if ext in DICOM_EXTS:
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dir_path = Path(filepath).resolve().parent
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reader = sitk.ImageSeriesReader()
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reader.MetaDataDictionaryArrayUpdateOn()
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reader.LoadPrivateTagsOn()
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series_files = reader.GetGDCMSeriesFileNames(
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str(dir_path), series_id)
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reader.SetFileNames(series_files)
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image = reader.Execute()
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name = dir_path.name
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elif ext in SEQUENCE_EXTS:
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image = sitk.ReadImage(filepath)
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if image.GetDimension() == 2:
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sequence = collect_image_sequence(filepath)
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image = sitk.ReadImage(sequence)
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name = get_sequence_name(filepath)
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else:
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image = sitk.ReadImage(filepath)
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name = Path(filepath).name.removesuffix(ext)
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else:
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image = sitk.ReadImage(filepath)
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name = Path(filepath).name.removesuffix(ext)
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return image, name
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def rgb2gray(image):
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# Convert sRGB image to gray scale and rescale results to [0,255]
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channels = [sitk.VectorIndexSelectionCast(
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image, i, sitk.sitkFloat32) for i in range(image.GetNumberOfComponentsPerPixel())]
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# linear mapping
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I = (0.2126*channels[0] + 0.7152*channels[1] + 0.0722*channels[2])
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return sitk.Cast(I, sitk.sitkFloat32)
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def x2gray(image):
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return sitk.VectorIndexSelectionCast(image, 0, sitk.sitkUInt16)
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class ImportVolumeDataDialog(bpy.types.Operator):
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bl_idname = "bioxelnodes.import_volume_data_dialog"
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bl_label = "Volume Data as Bioxels"
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bl_description = "Import Volume Data as Bioxels (VDB)"
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bl_options = {'UNDO'}
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filepath: bpy.props.StringProperty(
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subtype="FILE_PATH",
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options={'HIDDEN'}
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) # type: ignore
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series_id: bpy.props.StringProperty() # type: ignore
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resample_method: bpy.props.EnumProperty(
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name="Resample Method",
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default="linear",
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items=[("linear", "Linear", ""),
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("nearest_neighbor", "Nearest Neighbor", ""),
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("gaussian", "Gaussian", "")]
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) # type: ignore
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read_as: bpy.props.EnumProperty(
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name="Read as",
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default="scalar",
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items=[("scalar", "Scalar", ""),
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("labels", "Labels", "")]
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) # type: ignore
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label_index: bpy.props.IntProperty(
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name="Label Index",
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default=1
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) # type: ignore
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bioxel_size: bpy.props.FloatProperty(
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name="Bioxel Size (Larger size means small resolution)",
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soft_min=0.1, soft_max=10.0,
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min=1e-2, max=1e2,
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default=1,
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) # type: ignore
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orig_spacing: bpy.props.FloatVectorProperty(
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name="Original Spacing",
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default=(1, 1, 1),
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) # type: ignore
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orig_shape: bpy.props.IntVectorProperty(
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name="Original Shape",
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default=(100, 100, 100)
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) # type: ignore
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scene_scale: bpy.props.FloatProperty(
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name="Scene Scale (Bioxels Unit pre Blender Unit)",
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soft_min=0.001, soft_max=100.0,
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min=1e-6, max=1e6,
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default=0.01,
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) # type: ignore
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do_orient: bpy.props.BoolProperty(
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name="Orient to RAS",
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default=True,
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) # type: ignore
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invert_scalar: bpy.props.BoolProperty(
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name="Invert Scalar (Background value maybe higher than object)",
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default=False,
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) # type: ignore
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def execute(self, context):
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image, bioxels_name = read_image(self.filepath, self.series_id)
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bioxel_size = self.bioxel_size
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orig_spacing = self.orig_spacing
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image_spacing = image.GetSpacing()
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image_shape = image.GetSize()
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bioxels_spacing = (
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image_spacing[0] / orig_spacing[0] * bioxel_size,
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image_spacing[1] / orig_spacing[1] * bioxel_size,
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image_spacing[2] / orig_spacing[2] * bioxel_size
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)
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bioxels_shape = get_bioxels_shape(
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bioxel_size, image_shape, orig_spacing)
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if self.read_as == "labels":
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if "vector" in image.GetPixelIDTypeAsString():
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print("Convet to Grayscale...")
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image = x2gray(image)
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else:
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image = sitk.Cast(image, sitk.sitkUInt16)
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default_value = 0
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elif self.read_as == "scalar":
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if "vector" in image.GetPixelIDTypeAsString():
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print("Convet to Grayscale...")
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image = rgb2gray(image)
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else:
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image = sitk.Cast(image, sitk.sitkFloat32)
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stats = sitk.StatisticsImageFilter()
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stats.Execute(image)
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default_value = stats.GetMaximum() if self.invert_scalar else stats.GetMinimum()
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if self.resample_method == "linear":
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interpolator = sitk.sitkLinear
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elif self.resample_method == "nearest_neighbor":
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interpolator = sitk.sitkNearestNeighbor
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elif self.resample_method == "gaussian":
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interpolator = sitk.sitkGaussian
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print(f"Resampling...")
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image = sitk.Resample(
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image1=image,
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size=bioxels_shape,
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transform=sitk.Transform(),
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interpolator=interpolator,
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outputOrigin=image.GetOrigin(),
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outputSpacing=bioxels_spacing,
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outputDirection=image.GetDirection(),
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defaultPixelValue=default_value,
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outputPixelType=image.GetPixelID(),
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)
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if self.do_orient:
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print("Orienting to RAS...")
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image = sitk.DICOMOrient(image, 'RAS')
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print("Oriented Origin:", image.GetOrigin())
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print("Oriented Direction:", image.GetDirection())
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# return {'FINISHED'}
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# ITK indices, by convention, are [i,j,k] while NumPy indices are [k,j,i]
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# https://www.slicer.org/wiki/Coordinate_systems
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# ITK Numpy 3D
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# R (ight) i -> k -> x
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# A (nterior) j -> j -> y
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# S (uperior) k -> i -> z
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array = sitk.GetArrayFromImage(image)
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orig_dtype = str(array.dtype)
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# print(f"Coverting Dtype from {orig_dtype} to float...")
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# array = array.astype(float)
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if array.ndim == 4:
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# if array.shape[0] == 3 and self.read_as == "scalar":
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# # RGB -> Grayscale
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# array = np.dot(array[..., :3], [0.2989, 0.5870, 0.1140])
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# else:
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# array = array[:, :, :, 0]
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array = array[:, :, :, 0]
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array = np.transpose(array)
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bioxels_shape = array.shape
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bioxels_offset = 0.0
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if self.read_as == "labels":
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array = array == np.full_like(array, self.label_index)
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bioxels_default_threshold = 1.0
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bioxels_max = 1.0
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bioxels_min = 0.0
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bioxels_name = f"{bioxels_name}_{self.label_index}"
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else:
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if self.invert_scalar:
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array = -array
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orig_max = float(np.max(array))
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orig_min = float(np.min(array))
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orig_median = float(np.median(array))
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orig_percentile80 = float(np.percentile(array, 80)) \
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if self.invert_scalar else float(np.percentile(array, 80))
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# if (orig_dtype[0] != "u" and orig_min < 0) \
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# or (orig_dtype[0] == "u" and self.invert_scalar):
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if orig_min < 0:
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bioxels_offset = -orig_min
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array = array + np.full_like(array, bioxels_offset)
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bioxels_default_threshold = orig_percentile80
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bioxels_max = float(np.max(array))
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bioxels_min = float(np.min(array))
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stats_table = [("Max", orig_max),
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("Min", orig_min),
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("Median", orig_median),
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("80%", orig_percentile80)]
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print("Bioxels Value Stats:")
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for stats in stats_table:
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print("| {: >10} | {: >40} |".format(*stats))
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# # Build VDB
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grid = vdb.BoolGrid() if self.read_as == "labels" else vdb.FloatGrid()
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grid.copyFromArray(array.copy().astype(float))
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# After sitk.DICOMOrient(), origin and direction will also orient base on LPS
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# so we need to convert them into RAS
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mat_lps2ras = axis_conversion(
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from_forward='-Z',
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from_up='-Y',
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to_forward='-Z',
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to_up='Y'
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).to_4x4()
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origin = image.GetOrigin()
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direction = image.GetDirection()
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mat_location = mathutils.Matrix.Translation(
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mathutils.Vector(origin)
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)
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mat_rotation = mathutils.Matrix(
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np.array(direction).reshape((3, 3))
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).to_4x4()
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mat_scale = mathutils.Matrix.Scale(
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bioxel_size, 4
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)
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transfrom = mat_lps2ras @ mat_location @ mat_rotation @ mat_scale \
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if self.do_orient else mat_location @ mat_rotation @ mat_scale
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grid.transform = vdb.createLinearTransform(transfrom.transposed())
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grid.name = "scalar"
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preferences = context.preferences.addons[__package__].preferences
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vdb_dirpath = Path(preferences.cache_dir, 'VDBs')
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vdb_dirpath.mkdir(parents=True, exist_ok=True)
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vdb_path = Path(vdb_dirpath, f"{uuid4()}.vdb")
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print(f"Storing the VDB file ({str(vdb_path)})...")
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vdb.write(str(vdb_path), grids=[grid])
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# Read VDB
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print(f"Importing the VDB file to Blender scene...")
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bpy.ops.object.volume_import(
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filepath=str(vdb_path), align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
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bioxels_obj = bpy.context.active_object
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# Set props to VDB object
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bioxels_obj.name = f"{bioxels_name}_Bioxels"
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bioxels_obj.data.name = f"{bioxels_name}_Bioxels"
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# Make transformation
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scene_scale = float(self.scene_scale)
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# (S)uperior -Z -> Y
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# (A)osterior Y -> Z
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mat_ras2blender = axis_conversion(
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from_forward='-Z',
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from_up='Y',
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to_forward='Y',
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to_up='Z'
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).to_4x4()
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mat_scene_scale = mathutils.Matrix.Scale(
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scene_scale, 4
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)
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bioxels_obj.matrix_world = mat_ras2blender @ mat_scene_scale
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bioxels_obj.lock_location[0] = True
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bioxels_obj.lock_location[1] = True
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bioxels_obj.lock_location[2] = True
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bioxels_obj.lock_rotation[0] = True
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bioxels_obj.lock_rotation[1] = True
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bioxels_obj.lock_rotation[2] = True
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bioxels_obj.lock_scale[0] = True
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bioxels_obj.lock_scale[1] = True
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bioxels_obj.lock_scale[2] = True
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bioxels_obj.hide_select = True
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bioxels_obj['bioxels'] = True
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bpy.ops.node.new_geometry_nodes_modifier()
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node_tree = bioxels_obj.modifiers[0].node_group
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# Wrapper a Container
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bpy.ops.mesh.primitive_cube_add(
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enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1)
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)
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container_obj = bpy.context.active_object
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bbox_verts = calc_bbox_verts((0, 0, 0), bioxels_shape)
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for index, vert in enumerate(container_obj.data.vertices):
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bbox_transform = mat_ras2blender @ mat_scene_scale @ transfrom
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vert.co = bbox_transform @ mathutils.Vector(bbox_verts[index])
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bioxels_obj.parent = container_obj
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container_obj.name = bioxels_name
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container_obj.data.name = bioxels_name
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container_obj.visible_camera = False
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container_obj.visible_diffuse = False
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container_obj.visible_glossy = False
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container_obj.visible_transmission = False
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container_obj.visible_volume_scatter = False
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container_obj.visible_shadow = False
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container_obj.display_type = 'WIRE'
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container_obj['bioxels_container'] = True
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container_obj['scene_scale'] = scene_scale
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container_obj['bioxel_size'] = bioxel_size
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container_obj['bioxels_max'] = bioxels_max
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container_obj['bioxels_min'] = bioxels_min
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container_obj['bioxels_offset'] = bioxels_offset
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container_obj['bioxels_shape'] = bioxels_shape
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bpy.ops.object.modifier_add(type='NODES')
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container_obj.modifiers[0].node_group = node_tree
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container_obj.modifiers[0].show_in_editmode = False
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container_obj.modifiers[0].show_viewport = False
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container_obj.modifiers[0].show_render = False
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# Create BioxelNodes to VDB object
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print(f"Creating BioxelNodes to the VDB...")
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if preferences.do_add_segmentnode:
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nodes = node_tree.nodes
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links = node_tree.links
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input_node = get_node_by_type(nodes, 'NodeGroupInput')[0]
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output_node = get_node_by_type(nodes, 'NodeGroupOutput')[0]
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segment_node = custom_nodes.add_node(
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nodes, 'BioxelNodes_Segment')
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segment_node.inputs['Threshold'].default_value = bioxels_default_threshold
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links.new(input_node.outputs[0], segment_node.inputs[0])
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links.new(segment_node.outputs[0], output_node.inputs[0])
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# Change render setting for better result
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if preferences.do_change_render_setting:
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bpy.context.scene.render.engine = 'CYCLES'
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bpy.context.scene.cycles.volume_bounces = 12
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bpy.context.scene.cycles.transparent_max_bounces = 64
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self.report({"INFO"}, "Successfully Imported")
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|
|
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(
|
|
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:,} "
|
|
if bioxel_count > 100000000:
|
|
text += "**TOO LARGE!**"
|
|
|
|
panel = layout.box()
|
|
panel.prop(self, "resample_method")
|
|
panel.prop(self, "bioxel_size")
|
|
row = panel.row()
|
|
row.prop(self, "orig_spacing")
|
|
panel.label(text=text)
|
|
|
|
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):
|
|
items = []
|
|
for index, series_id in enumerate(self.series_ids):
|
|
items.append((
|
|
series_id.id,
|
|
series_id.label,
|
|
"",
|
|
index
|
|
))
|
|
|
|
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)"
|
|
bl_options = {'UNDO'}
|
|
|
|
filepath: bpy.props.StringProperty(subtype="FILE_PATH") # type: ignore
|
|
directory: bpy.props.StringProperty(subtype='DIR_PATH') # type: ignore
|
|
|
|
series_id: bpy.props.EnumProperty(
|
|
name="Select Series",
|
|
items=get_series_ids
|
|
) # type: ignore
|
|
|
|
series_ids: bpy.props.CollectionProperty(
|
|
type=BIOXELNODES_Series) # type: ignore
|
|
|
|
def execute(self, context):
|
|
ext = get_ext(self.filepath)
|
|
if ext not in SUPPORT_EXTS:
|
|
self.report({"WARNING"}, "Not supported extension.")
|
|
return {'CANCELLED'}
|
|
|
|
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())]
|
|
|
|
print("Meta Data:")
|
|
for stats in stats_table:
|
|
print("| {: >10} | {: >40} |".format(*stats))
|
|
|
|
do_orient = ext not in SEQUENCE_EXTS or ext in DICOM_EXTS
|
|
|
|
bpy.ops.bioxelnodes.import_volume_data_dialog(
|
|
'INVOKE_DEFAULT',
|
|
filepath=self.filepath,
|
|
orig_shape=image.GetSize(),
|
|
orig_spacing=image.GetSpacing(),
|
|
series_id=self.series_id or "",
|
|
do_orient=do_orient
|
|
)
|
|
|
|
self.report({"INFO"}, "Successfully Readed.")
|
|
|
|
return {'FINISHED'}
|
|
|
|
def modal(self, context, event):
|
|
self.execute(context)
|
|
return {'FINISHED'}
|
|
|
|
def invoke(self, context, event):
|
|
if not self.filepath and not self.directory:
|
|
return {'CANCELLED'}
|
|
|
|
show_message('Reading image data, it may take a while...',
|
|
'Please be patient...')
|
|
|
|
if get_ext(self.filepath) == '.dcm':
|
|
dir_path = Path(self.filepath).parent
|
|
reader = sitk.ImageSeriesReader()
|
|
reader.MetaDataDictionaryArrayUpdateOn()
|
|
reader.LoadPrivateTagsOn()
|
|
series_ids = reader.GetGDCMSeriesIDs(str(dir_path))
|
|
|
|
for _id in series_ids:
|
|
series_id = self.series_ids.add()
|
|
series_id.id = _id
|
|
series_id.label = _id
|
|
|
|
if len(series_ids) > 1:
|
|
context.window_manager.invoke_props_dialog(self, width=400)
|
|
return {'RUNNING_MODAL'}
|
|
else:
|
|
self.series_id = series_ids[0]
|
|
|
|
context.window_manager.modal_handler_add(self)
|
|
return {'RUNNING_MODAL'}
|
|
|
|
def draw(self, context):
|
|
layout = self.layout
|
|
layout.prop(self, "series_id")
|
|
layout.label(
|
|
text="Reading image data, it may take a while...")
|
|
layout.label(
|
|
text="Please be patient...")
|
|
|
|
|
|
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_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(
|
|
'INVOKE_DEFAULT',
|
|
filepath=self.filepath,
|
|
directory=self.directory
|
|
)
|
|
return {'FINISHED'}
|
|
|
|
def invoke(self, context, event):
|
|
context.window_manager.fileselect_add(self)
|
|
return {'RUNNING_MODAL'}
|
|
|
|
|
|
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_file_extensions = ";".join(FH_EXTS)
|
|
|
|
@classmethod
|
|
def poll_drop(cls, context):
|
|
return (context.area and context.area.type == 'VIEW_3D')
|
|
except:
|
|
...
|
|
|
|
|
|
class ExportVDB(bpy.types.Operator):
|
|
bl_idname = "bioxelnodes.export_vdb"
|
|
bl_label = "Bioxels as VDB"
|
|
bl_description = "Export Bioxels original VDB data"
|
|
bl_options = {'UNDO'}
|
|
|
|
filepath: bpy.props.StringProperty(
|
|
subtype="FILE_PATH"
|
|
) # type: ignore
|
|
|
|
filename_ext = ".vdb"
|
|
|
|
@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 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
|
|
|
|
filepath = f"{self.filepath.split('.')[0]}.vdb"
|
|
# "//"
|
|
source_dir = bpy.path.abspath(bioxels_obj.data.filepath)
|
|
|
|
output_path: Path = Path(filepath).resolve()
|
|
source_path: Path = Path(source_dir).resolve()
|
|
# print('output_path', output_path)
|
|
# print('source_path', source_path)
|
|
shutil.copy(source_path, output_path)
|
|
|
|
self.report({"INFO"}, f"Successfully exported to {output_path}")
|
|
|
|
return {'FINISHED'}
|