783 lines
26 KiB
Python
783 lines
26 KiB
Python
import math
|
|
import bpy
|
|
import shutil
|
|
from bpy_extras.io_utils import axis_conversion
|
|
import pyopenvdb as vdb
|
|
import numpy as np
|
|
from pathlib import Path
|
|
from uuid import uuid4
|
|
import mathutils
|
|
import random
|
|
|
|
from . import skimage as ski
|
|
from .nodes import custom_nodes
|
|
from .props import BIOXELNODES_Series
|
|
from .utils import (calc_bbox_verts, get_all_layers, get_container_from_selection, get_layer, get_text_index_str,
|
|
get_node_by_type, hide_in_ray, lock_transform, save_vdb, show_message)
|
|
|
|
try:
|
|
import SimpleITK as sitk
|
|
except:
|
|
...
|
|
|
|
SUPPORT_EXTS = ['', '.dcm', '.DCM', '.DICOM',
|
|
'.bmp', '.BMP',
|
|
'.PIC', '.pic',
|
|
'.gipl', '.gipl.gz',
|
|
'.jpg', '.JPG', '.jpeg', '.JPEG',
|
|
'.lsm', '.LSM',
|
|
'.tif', '.TIF', '.tiff', '.TIFF',
|
|
'.mnc', '.MNC',
|
|
'.mrc', '.rec',
|
|
'.mha', '.mhd',
|
|
'.hdf', '.h4', '.hdf4', '.he2', '.h5', '.hdf5', '.he5',
|
|
'.nia', '.nii', '.nii.gz', '.hdr', '.img', '.img.gz',
|
|
'.nrrd', '.nhdr',
|
|
'.png', '.PNG',
|
|
'.vtk']
|
|
|
|
SEQUENCE_EXTS = ['.dcm', '.DCM', '.DICOM',
|
|
'.bmp', '.BMP',
|
|
'.jpg', '.JPG', '.jpeg', '.JPEG',
|
|
'.tif', '.TIF', '.tiff', '.TIFF',
|
|
'.png', '.PNG']
|
|
|
|
DICOM_EXTS = ['', '.dcm', '.DCM', '.DICOM']
|
|
|
|
FH_EXTS = ['', '.dcm', '.DCM', '.DICOM',
|
|
'.gipl', '.gipl.gz',
|
|
'.mnc', '.MNC',
|
|
'.mrc', '.rec',
|
|
'.mha', '.mhd',
|
|
'.nia', '.nii', '.nii.gz', '.hdr', '.img', '.img.gz',
|
|
'.hdf', '.h4', '.hdf4', '.he2', '.h5', '.hdf5', '.he5',
|
|
'.nrrd', '.nhdr',
|
|
'.vtk',
|
|
'.gz']
|
|
|
|
|
|
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]))
|
|
|
|
return (shape[0] if shape[0] > 0 else 1,
|
|
shape[1] if shape[1] > 0 else 1,
|
|
shape[2] if shape[2] > 0 else 1)
|
|
|
|
|
|
def get_layer_size(shape: tuple, bioxel_size: float, scale: float = 1.0):
|
|
size = (float(shape[0] * bioxel_size * scale),
|
|
float(shape[1] * bioxel_size * scale),
|
|
float(shape[2] * bioxel_size * scale))
|
|
|
|
return size
|
|
|
|
|
|
def get_ext(filepath: str) -> str:
|
|
file_path = Path(filepath)
|
|
if file_path.name.endswith(".nii.gz"):
|
|
return ".nii.gz"
|
|
elif file_path.name.endswith(".img.gz"):
|
|
return ".img.gz"
|
|
elif file_path.name.endswith(".gipl.gz"):
|
|
return ".gipl.gz"
|
|
else:
|
|
return file_path.suffix
|
|
|
|
|
|
def get_sequence_name(filepath: str) -> str:
|
|
ext = get_ext(filepath)
|
|
filename = Path(filepath).name.removesuffix(ext)
|
|
index: str = get_text_index_str(filename)
|
|
return filename.removesuffix(index)
|
|
|
|
|
|
def get_sequence_index(filepath: str) -> int:
|
|
ext = get_ext(filepath)
|
|
filename = Path(filepath).name.removesuffix(ext)
|
|
index: str = get_text_index_str(filename)
|
|
return int(index) if index else 0
|
|
|
|
|
|
def collect_sequence(filepath: str):
|
|
file_path = Path(filepath).resolve()
|
|
|
|
files = list(file_path.parent.iterdir())
|
|
files = [f for f in files if f.is_file()
|
|
and get_ext(file_path) == get_ext(f)
|
|
and get_sequence_name(file_path) == get_sequence_name(f)]
|
|
|
|
files.sort(key=get_sequence_index)
|
|
sequence = [str(f) for f in files]
|
|
return sequence
|
|
|
|
|
|
def parse_volume_data(filepath: str, series_id=""):
|
|
ext = get_ext(filepath)
|
|
|
|
if ext in DICOM_EXTS:
|
|
dir_path = Path(filepath).resolve().parent
|
|
reader = sitk.ImageSeriesReader()
|
|
reader.MetaDataDictionaryArrayUpdateOn()
|
|
reader.LoadPrivateTagsOn()
|
|
series_files = reader.GetGDCMSeriesFileNames(
|
|
str(dir_path), series_id)
|
|
reader.SetFileNames(series_files)
|
|
itk_volume = reader.Execute()
|
|
name = dir_path.name
|
|
|
|
elif ext in SEQUENCE_EXTS:
|
|
itk_volume = sitk.ReadImage(filepath)
|
|
if itk_volume.GetDimension() == 2:
|
|
sequence = collect_sequence(filepath)
|
|
itk_volume = sitk.ReadImage(sequence)
|
|
name = get_sequence_name(filepath)
|
|
else:
|
|
itk_volume = sitk.ReadImage(filepath)
|
|
name = Path(filepath).name.removesuffix(ext)
|
|
else:
|
|
itk_volume = sitk.ReadImage(filepath)
|
|
name = Path(filepath).name.removesuffix(ext)
|
|
|
|
itk_volume = sitk.DICOMOrient(itk_volume, 'RAS')
|
|
volume = sitk.GetArrayFromImage(itk_volume)
|
|
|
|
if volume.ndim == 4:
|
|
volume = np.transpose(volume, (2, 1, 0, 3))
|
|
else:
|
|
volume = np.transpose(volume)
|
|
|
|
meta = {
|
|
"name": name,
|
|
"shape": tuple(itk_volume.GetSize()),
|
|
"spacing": tuple(itk_volume.GetSpacing()),
|
|
"origin": tuple(itk_volume.GetOrigin()),
|
|
"direction": tuple(itk_volume.GetDirection()),
|
|
}
|
|
|
|
for key, value in meta.items():
|
|
print(f"{key}: {value}")
|
|
|
|
return volume, meta
|
|
|
|
|
|
class ImportVolumeDataDialog(bpy.types.Operator):
|
|
bl_idname = "bioxelnodes.import_volume_data_dialog"
|
|
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
|
|
|
|
container_name: bpy.props.StringProperty(
|
|
name="Container Name"
|
|
) # type: ignore
|
|
|
|
layer_name: bpy.props.StringProperty(
|
|
name="Layer Name",
|
|
) # type: ignore
|
|
|
|
series_id: bpy.props.StringProperty() # type: ignore
|
|
|
|
container: bpy.props.StringProperty() # type: ignore
|
|
|
|
read_as: bpy.props.EnumProperty(
|
|
name="Read as",
|
|
default="scalar",
|
|
items=[("scalar", "Scalar", ""),
|
|
("labels", "Labels", "")]
|
|
) # type: ignore
|
|
|
|
bioxel_size: bpy.props.FloatProperty(
|
|
name="Bioxel Size (Larger size means small resolution)",
|
|
soft_min=0.1, soft_max=10.0,
|
|
min=0.1, max=1e2,
|
|
default=1,
|
|
) # type: ignore
|
|
|
|
orig_spacing: bpy.props.FloatVectorProperty(
|
|
name="Original Spacing",
|
|
default=(1, 1, 1),
|
|
) # type: ignore
|
|
|
|
orig_shape: bpy.props.IntVectorProperty(
|
|
name="Original Shape",
|
|
default=(100, 100, 100)
|
|
) # type: ignore
|
|
|
|
scene_scale: bpy.props.FloatProperty(
|
|
name="Scene Scale (Bioxel Unit pre Blender Unit)",
|
|
soft_min=0.0001, soft_max=10.0,
|
|
min=1e-6, max=1e6,
|
|
default=0.01,
|
|
) # type: ignore
|
|
|
|
do_orient: bpy.props.BoolProperty(
|
|
name="Orient to RAS",
|
|
default=True,
|
|
) # type: ignore
|
|
|
|
def execute(self, context):
|
|
is_first_import = len(get_all_layers()) == 0
|
|
volume, meta = parse_volume_data(self.filepath)
|
|
container_name = self.container_name or meta['name'] or "Container"
|
|
bioxel_size = self.bioxel_size
|
|
orig_spacing = self.orig_spacing
|
|
|
|
layer_spacing = (
|
|
meta['spacing'][0] / orig_spacing[0] * bioxel_size,
|
|
meta['spacing'][1] / orig_spacing[1] * bioxel_size,
|
|
meta['spacing'][2] / orig_spacing[2] * bioxel_size
|
|
)
|
|
|
|
layer_shape = get_layer_shape(
|
|
bioxel_size, meta['shape'], orig_spacing)
|
|
|
|
# After sitk.DICOMOrient(), origin and direction will also orient base on LPS
|
|
# so we need to convert them into RAS
|
|
mat_lps2ras = axis_conversion(
|
|
from_forward='-Z',
|
|
from_up='-Y',
|
|
to_forward='-Z',
|
|
to_up='Y'
|
|
).to_4x4()
|
|
|
|
mat_location = mathutils.Matrix.Translation(
|
|
mathutils.Vector(meta['origin'])
|
|
)
|
|
|
|
mat_rotation = mathutils.Matrix(
|
|
np.array(meta['direction']).reshape((3, 3))
|
|
).to_4x4()
|
|
|
|
mat_scale = mathutils.Matrix.Scale(
|
|
bioxel_size, 4
|
|
)
|
|
|
|
# transfrom = mat_lps2ras @ mat_location @ mat_rotation @ mat_scale \
|
|
# if self.do_orient else mat_location @ mat_rotation @ mat_scale
|
|
|
|
transfrom = mat_lps2ras @ mat_location @ mat_rotation @ mat_scale
|
|
|
|
# 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), volume.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])
|
|
|
|
else:
|
|
container = bpy.data.objects[self.container]
|
|
container_node_tree = container.modifiers[0].node_group
|
|
|
|
preferences = context.preferences.addons[__package__].preferences
|
|
loc, rot, sca = transfrom.decompose()
|
|
|
|
layer_origin = tuple(loc)
|
|
layer_rotation = tuple(rot.to_euler())
|
|
|
|
def create_layer(volume, layer_name, layer_type="scalar"):
|
|
grid = vdb.FloatGrid()
|
|
volume = volume.copy().astype(np.float32)
|
|
grid.copyFromArray(volume)
|
|
grid.transform = vdb.createLinearTransform(transfrom.transposed())
|
|
grid.name = layer_type
|
|
|
|
vdb_path = save_vdb([grid], context)
|
|
|
|
# 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))
|
|
|
|
layer = bpy.context.active_object
|
|
|
|
# Set props to VDB object
|
|
layer.name = layer_name
|
|
layer.data.name = layer_name
|
|
|
|
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
|
|
|
|
layer['bioxel_layer'] = True
|
|
layer['bioxel_layer_type'] = layer_type
|
|
layer.parent = container
|
|
|
|
for collection in layer.users_collection:
|
|
collection.objects.unlink(layer)
|
|
|
|
for collection in container.users_collection:
|
|
collection.objects.link(layer)
|
|
|
|
print(f"Creating layer ...")
|
|
|
|
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]
|
|
|
|
to_layer_node = custom_nodes.add_node(nodes,
|
|
"BioxelNodes__ConvertToLayer")
|
|
|
|
links.new(input_node.outputs[0], to_layer_node.inputs[0])
|
|
links.new(to_layer_node.outputs[0], output_node.inputs[0])
|
|
|
|
to_layer_node.inputs['Layer ID'].default_value = random.randint(-200000000,
|
|
200000000)
|
|
to_layer_node.inputs['Bioxel Size'].default_value = bioxel_size
|
|
to_layer_node.inputs['Shape'].default_value = layer_shape
|
|
to_layer_node.inputs['Origin'].default_value = layer_origin
|
|
to_layer_node.inputs['Rotation'].default_value = layer_rotation
|
|
|
|
return layer
|
|
|
|
if self.read_as == "labels":
|
|
if volume.ndim == 4:
|
|
volume = np.amax(volume, -1)
|
|
volume = volume.astype(int)
|
|
orig_max = int(np.max(volume))
|
|
orig_min = int(np.min(volume))
|
|
layer_name = self.layer_name or "Label"
|
|
|
|
for i in range(orig_max):
|
|
label = volume == np.full_like(volume, i+1)
|
|
print(f"Resampling...")
|
|
label = ski.resize(label.astype(np.float32),
|
|
layer_shape,
|
|
anti_aliasing=True)
|
|
layer = create_layer(volume=label,
|
|
layer_name=f"{container_name}_{layer_name}_{i+1}",
|
|
layer_type="label")
|
|
|
|
# Deselect all nodes first
|
|
for node in container_node_tree.nodes:
|
|
if node.select:
|
|
node.select = False
|
|
|
|
mask_node = custom_nodes.add_node(container_node_tree.nodes,
|
|
'BioxelNodes_MaskByLabel')
|
|
mask_node.label = f"{layer_name}_{i+1}"
|
|
mask_node.inputs[0].default_value = layer
|
|
|
|
# Connect to output if no output linked
|
|
output_node = get_node_by_type(container_node_tree.nodes,
|
|
'NodeGroupOutput')[0]
|
|
if len(output_node.inputs[0].links) == 0:
|
|
container_node_tree.links.new(mask_node.outputs[0],
|
|
output_node.inputs[0])
|
|
|
|
else:
|
|
if volume.ndim == 4:
|
|
volume = np.amax(volume, -1)
|
|
# volume = skimage.color.rgb2gray(volume)
|
|
|
|
# if volume.dtype.kind == 'u':
|
|
# imax_in = np.iinfo(volume.dtype).max
|
|
# volume = np.multiply(volume, 255.0 / imax_in, dtype=np.float32)
|
|
# elif volume.dtype.kind == 'i':
|
|
# volume = volume.astype(np.float32)
|
|
|
|
# should not change any value!
|
|
volume = volume.astype(np.float32)
|
|
|
|
print(f"Resampling...")
|
|
volume = ski.resize(volume,
|
|
layer_shape,
|
|
anti_aliasing=True)
|
|
|
|
orig_max = float(np.max(volume))
|
|
orig_min = float(np.min(volume))
|
|
|
|
scalar_offset = 0
|
|
if orig_min < 0:
|
|
scalar_offset = -orig_min
|
|
volume = volume + np.full_like(volume, scalar_offset)
|
|
|
|
layer_name = self.layer_name or "Scalar"
|
|
layer = create_layer(volume=volume,
|
|
layer_name=f"{container_name}_{layer_name}",
|
|
layer_type="scalar")
|
|
|
|
layer_node_tree = layer.modifiers[0].node_group
|
|
to_layer_node = layer_node_tree.nodes['BioxelNodes__ConvertToLayer']
|
|
to_layer_node.inputs['Scalar Offset'].default_value = scalar_offset
|
|
to_layer_node.inputs['Scalar Max'].default_value = orig_max
|
|
to_layer_node.inputs['Scalar Min'].default_value = orig_min
|
|
|
|
# Deselect all nodes first
|
|
for node in container_node_tree.nodes:
|
|
if node.select:
|
|
node.select = False
|
|
mask_node = custom_nodes.add_node(container_node_tree.nodes,
|
|
'BioxelNodes_MaskByThreshold')
|
|
mask_node.label = layer_name
|
|
mask_node.inputs[0].default_value = layer
|
|
|
|
# Connect to output if no output linked
|
|
output_node = get_node_by_type(container_node_tree.nodes,
|
|
'NodeGroupOutput')[0]
|
|
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 and is_first_import:
|
|
bpy.context.scene.render.engine = 'CYCLES'
|
|
try:
|
|
bpy.context.scene.cycles.volume_bounces = 12
|
|
bpy.context.scene.cycles.transparent_max_bounces = 16
|
|
bpy.context.scene.cycles.volume_preview_step_rate = 10
|
|
bpy.context.scene.cycles.volume_step_rate = 10
|
|
bpy.context.scene.eevee.volumetric_tile_size = '2'
|
|
bpy.context.scene.eevee.volumetric_shadow_samples = 128
|
|
bpy.context.scene.eevee.volumetric_samples = 256
|
|
except:
|
|
pass
|
|
|
|
self.report({"INFO"}, "Successfully Imported")
|
|
|
|
return {'FINISHED'}
|
|
|
|
def invoke(self, context, event):
|
|
if self.read_as == "labels":
|
|
volume_dtype = "Label"
|
|
elif self.read_as == "scalar":
|
|
volume_dtype = "Scalar"
|
|
title = f"Import '{volume_dtype}' Layer (Add to Container: {self.container})" \
|
|
if self.container != "" else f"Import '{volume_dtype}' Layer (Init a Container)"
|
|
context.window_manager.invoke_props_dialog(self,
|
|
width=500,
|
|
title=title)
|
|
return {'RUNNING_MODAL'}
|
|
|
|
def draw(self, context):
|
|
layer_shape = get_layer_shape(self.bioxel_size,
|
|
self.orig_shape,
|
|
self.orig_spacing)
|
|
layer_size = get_layer_size(layer_shape,
|
|
self.bioxel_size,
|
|
self.scene_scale)
|
|
|
|
bioxel_count = layer_shape[0] * layer_shape[1] * layer_shape[2]
|
|
layer_shape_text = f"Shape will be: {str(layer_shape)} {bioxel_count:,} "
|
|
if bioxel_count > 100000000:
|
|
layer_shape_text += "**TOO LARGE!**"
|
|
|
|
layer_size_text = f"Size will be: ({layer_size[0]:.2f}, {layer_size[1]:.2f}, {layer_size[2]:.2f}) m"
|
|
|
|
layout = self.layout
|
|
panel = layout.box()
|
|
if self.container == "":
|
|
panel.prop(self, "container_name")
|
|
panel.prop(self, "layer_name")
|
|
|
|
panel = layout.box()
|
|
panel.prop(self, "bioxel_size")
|
|
row = panel.row()
|
|
row.prop(self, "orig_spacing")
|
|
panel.label(text=layer_shape_text)
|
|
|
|
if self.container == "":
|
|
panel = layout.box()
|
|
panel.prop(self, "scene_scale")
|
|
panel.label(text=layer_size_text)
|
|
|
|
|
|
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 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
|
|
|
|
read_as: bpy.props.EnumProperty(
|
|
name="Read as",
|
|
default="scalar",
|
|
items=[("scalar", "Scalar", ""),
|
|
("labels", "Labels", "")]
|
|
) # 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...")
|
|
volume, meta = parse_volume_data(self.filepath)
|
|
do_orient = ext not in SEQUENCE_EXTS or ext in DICOM_EXTS
|
|
|
|
orig_shape = meta['shape']
|
|
orig_spacing = meta['spacing']
|
|
min_size = min(orig_spacing[0], orig_spacing[1], orig_spacing[2])
|
|
bioxel_size = max(min_size, 1.0)
|
|
|
|
layer_size = get_layer_size(orig_shape,
|
|
bioxel_size)
|
|
log10 = math.floor(math.log10(max(*layer_size)))
|
|
scene_scale = math.pow(10, -log10)
|
|
|
|
if self.container:
|
|
container = bpy.data.objects[self.container]
|
|
container_name = container.name
|
|
else:
|
|
container_name = meta['name']
|
|
|
|
bpy.ops.bioxelnodes.import_volume_data_dialog(
|
|
'INVOKE_DEFAULT',
|
|
filepath=self.filepath,
|
|
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,
|
|
container=self.container,
|
|
read_as=self.read_as,
|
|
scene_scale=scene_scale
|
|
)
|
|
|
|
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():
|
|
bl_options = {'UNDO'}
|
|
|
|
filepath: bpy.props.StringProperty(subtype="FILE_PATH") # type: ignore
|
|
directory: bpy.props.StringProperty(subtype='DIR_PATH') # type: ignore
|
|
|
|
read_as = "scalar"
|
|
|
|
def execute(self, context):
|
|
containers = get_container_from_selection()
|
|
|
|
if len(containers) > 0:
|
|
bpy.ops.bioxelnodes.parse_volume_data(
|
|
'INVOKE_DEFAULT',
|
|
filepath=self.filepath,
|
|
directory=self.directory,
|
|
container=containers[0].name,
|
|
read_as=self.read_as
|
|
)
|
|
else:
|
|
bpy.ops.bioxelnodes.parse_volume_data(
|
|
'INVOKE_DEFAULT',
|
|
filepath=self.filepath,
|
|
directory=self.directory
|
|
)
|
|
|
|
return {'FINISHED'}
|
|
|
|
def invoke(self, context, event):
|
|
context.window_manager.fileselect_add(self)
|
|
return {'RUNNING_MODAL'}
|
|
|
|
|
|
class ImportAsScalarLayer(bpy.types.Operator, ImportVolumeData):
|
|
bl_idname = "bioxelnodes.import_as_scalar_layer"
|
|
bl_label = "Import as Scalar"
|
|
bl_description = "Import Volume Data to Container as Scalar"
|
|
read_as = "scalar"
|
|
|
|
|
|
class ImportAsLabelLayer(bpy.types.Operator, ImportVolumeData):
|
|
bl_idname = "bioxelnodes.import_as_label_layer"
|
|
bl_label = "Import as Labels"
|
|
bl_description = "Import Volume Data to Container as Label"
|
|
read_as = "labels"
|
|
|
|
|
|
try:
|
|
class BIOXELNODES_FH_ImportVolumeData(bpy.types.FileHandler):
|
|
bl_idname = "BIOXELNODES_FH_ImportVolumeData"
|
|
bl_label = "File handler for dicom import"
|
|
bl_import_operator = "bioxelnodes.parse_volume_data"
|
|
bl_file_extensions = ";".join(FH_EXTS)
|
|
|
|
@classmethod
|
|
def poll_drop(cls, context):
|
|
return (context.area and context.area.type == 'VIEW_3D')
|
|
except:
|
|
...
|
|
|
|
|
|
class AddVolumeData(bpy.types.Operator):
|
|
bl_idname = "bioxelnodes.add_volume_data"
|
|
bl_label = "Import as Bioxel Layer"
|
|
bl_description = "Import additional 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):
|
|
containers = get_container_from_selection()
|
|
return len(containers) > 0
|
|
|
|
def execute(self, context):
|
|
containers = get_container_from_selection()
|
|
|
|
bpy.ops.bioxelnodes.parse_volume_data(
|
|
'INVOKE_DEFAULT',
|
|
filepath=self.filepath,
|
|
directory=self.directory,
|
|
container=containers[0].name
|
|
)
|
|
return {'FINISHED'}
|
|
|
|
def invoke(self, context, event):
|
|
context.window_manager.fileselect_add(self)
|
|
return {'RUNNING_MODAL'}
|
|
|
|
|
|
class ExportVolumeData(bpy.types.Operator):
|
|
bl_idname = "bioxelnodes.export_volume_data"
|
|
bl_label = "Export Layer"
|
|
bl_description = "Export Bioxel Layer as VDB"
|
|
bl_options = {'UNDO'}
|
|
|
|
filepath: bpy.props.StringProperty(
|
|
subtype="FILE_PATH"
|
|
) # type: ignore
|
|
|
|
filename_ext = ".vdb"
|
|
|
|
@classmethod
|
|
def poll(cls, context):
|
|
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):
|
|
layer = get_layer(bpy.context.active_object)
|
|
|
|
filepath = f"{self.filepath.split('.')[0]}.vdb"
|
|
# "//"
|
|
source_dir = bpy.path.abspath(layer.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'}
|