diff --git a/.prettierrc b/.prettierrc new file mode 100644 index 0000000..ab27099 --- /dev/null +++ b/.prettierrc @@ -0,0 +1,11 @@ +{ + "tabWidth": 2, + "overrides": [ + { + "files": "*.md", + "options": { + "tabWidth": 4 + } + } + ] +} diff --git a/README.md b/README.md index 909cbc5..2c01e8c 100644 --- a/README.md +++ b/README.md @@ -15,96 +15,31 @@ Before us, there have been many tutorials and add-ons for importing volumetric d Below are some examples with Bioxel Nodes. Thanks to Cycles Render, the volumetric data can be rendered with great detail: -![gallery](docs/images/gallery.png) +![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) + +# Supported Format + +| Format | EXT | Test | +| ------ | ---------------------------------------- | ------- | +| DICOM | .dcm, .DICOM | ✅ pass | +| BMP | .bmp, .BMP | ✅ pass | +| JPEG | .jpg, .JPG, .jpeg, .JPEG | ✅ pass | +| PNG | .png, .PNG | ✅ pass | +| TIFF | .tif, .TIF, .tiff, .TIFF | ✅ pass | +| Nifti | .nia, .nii, .nii.gz, .hdr, .img, .img.gz | ✅ pass | +| Nrrd | .nrrd, .nhdr | ✅ pass | +| Meta | .mha, .mhd | yet | +| HDF5 | .hdf, .h4, .hdf4, .he2, .h5, .hdf5, .he5 | ✅ pass | +| VTK | .vtk | yet | +| BioRad | .PIC, .pic | yet | +| Gipl | .gipl, .gipl.gz | yet | +| LSM | .lsm, .LSM | yet | +| MINC | .mnc, .MNC | yet | +| MRC | .mrc, .rec | yet | + +# Known limitations -### Known limitations - -- Cannot read DICOM with multiple series. - Sections cannot be generated -- Only sequence files are supported, packed volume data formats are not supported yet (will be supported soon) - -# Getting Started - -Currently only support Blender 4.1 or above, make sure you have the correct version of Blender. - -### Add-on Installation - -Download the latest version https://github.com/OmooLab/BioxelNodes/releases/latest -In Blender, `Edit - Preferences - Add-ons - Install`, select the `BioxelNodes_{version}.zip` you just downloaded. - -### Dependency Installation - -The add-on requires a third-party python dependency called SimpleITK, click the Install SimpleITK button below to install the dependency. After clicking, blender may get stuck, it is downloading and installing, just wait for a moment. After the Installation, **restart blender once**. - -![dependency](docs/images/dependency.png) - -This step may have failed due to network factors, just click "Set PyPI Mirror" to change the mirror. - -### Basic Usage - -First you need to have your volumetric data ready. If not, you can access open research data from [Dryad](https://datadryad.org) (Dryad publishes data exclusively under a [Creative Commons Public Domain License](https://creativecommons.org/public-domain/cc0/)) - -Note: Make sure one folder contains only one sequence, multiple sequences need to be manually split into different folders first. - -In Blender, `File - Import - Volume Data as Bioxels`, select **one** of the .dcm files and click on "Volume Data as Bioxels" (you can also drag one of the .dcm files directly into the 3D viewport to trigger the import, but this is limited to .dcm format files) - -![importing](docs/images/importing.png) - -It may take a while to read data. After finishing reading, it will pop up a dialog box - -![import dialog](docs/images/import_dialog.png) - -Ignore the options, just click OK! - -After importing, the necessary nodes are automatically added, the reconstruction and shader are created, and then turned on the cycles rendering to directly see the result. - -![result](docs/images/result.png) - -Click select Bioxels Object, and open the Geometry Nodes panel to see the following node graph: - -![segment node](docs/images/segment_node.png) - -You can change the "Threshold" to modify the reconstruction model, or change the "Color", "Density" to modify the shader effect. All the parameters are straightforward, you can understand them by changing the values. - -The node, that named "Segment", is a preset node that combines the steps of 3D reconstruction process and shading process. In general, you need to add one of the segmentation node to reconstruction first, and followed by one of the shader node to set the shader. As you can see in the following figure: - -![general graph](docs/images/general_graph.png) - -Currently there are 3 types of nodes - -- Segmentation nodes, responsible for splitting the volume into a reconstructed model (we call them "Segment"). -- Shader nodes, responsible for giving shader to the Segment. -- Slicer nodes, responsible for partially cutting the Segment. - -For example: - -![general graph example](docs/images/general_graph_example.png) - -You can add a "Bake" node between segmentation node and shader node, if the reconstruction process consumes too much computing time. But be sure, you are selecting the volume object, not the container object. - -![bake node](docs/images/bake_node.png) - -# Future Features - -- Support more volumetric data formats (.nii, .map, .txm...) -- Generate sections -- More segmentation methods, e.g. AI segmentation. -- Even better shader for volumetric rendering - -# Technical Notes - -The "Bioxel" in "BioxelNodes", is a combination of the words "Bio-" and "Voxel". Bioxel is a voxel that stores biological data, so maybe its chinese name should be "生素" 😂? 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. - -### Bioxels - -Bioxels is based on the RAS coordinate system, Right Aanterior Superior, which was chosen over LPS because it is more compatible with most 3D CG software coordinate systems, and is in line with the 3D artist's understanding of space. - -All distances within Bioxels are in Units, and are specified in Meter pre unit. However, when Bioxels is imported into 3D CG software, its size in the software is not scaled by reading the Meter pre unit directly. The reason for this is that many 3D operations in software require that the primtives not be too large or too small. - -### Based on OpenVDB - -Bioxels is based entirely on OpenVDB for storage and rendering. The main reason for choosing OpenVDB is that as a volumetric data format, it is the fastest way to work with most CG renderers. - -### Based on Geometry Nodes - -Bioxel Nodes relies on Blender Geometry Nodes to reconstruct and render volumetric data. Node-based operations ensure that the original data is not permanently altered during reconstruction and rendering operations. The fact that the processing is based on Geometry Nodes without any additional dependencies also ensures that Blender can open files without this plugin installed. Look for more support for OpenVDB in GeometryNodes so that Bioxel Nodes can do more in the future. +- Time sequence volume not supported (will be supported soon) diff --git a/bioxelnodes/__init__.py b/bioxelnodes/__init__.py index aa34072..999d860 100644 --- a/bioxelnodes/__init__.py +++ b/bioxelnodes/__init__.py @@ -1,16 +1,15 @@ -from .nodes import custom_nodes -from . import auto_load -from . import menu - import bpy +from . import auto_load +from . import menus + bl_info = { "name": "Bioxel Nodes", "author": "Ma Nan", "description": "", - "blender": (4, 1, 0), - "version": (0, 1, 0), + "blender": (4, 0, 0), + "version": (0, 1, 1), "location": "File -> Import", "warning": "", "category": "Node" @@ -18,23 +17,17 @@ auto_load.init() -bpy.types.Scene.bioxels_dir = bpy.props.StringProperty( - name="Bioxels Directory", - subtype='DIR_PATH', - default="//" -) - def register(): auto_load.register() - custom_nodes.register() - menu.create_menu() + menus.add() + bpy.types.Scene.bioxels_dir = bpy.props.StringProperty( + name="Bioxels Directory", + subtype='DIR_PATH', + default="//" + ) def unregister(): - try: - menu.remove_menu() - custom_nodes.unregister() - auto_load.unregister() - except RuntimeError: - pass + menus.remove() + auto_load.unregister() diff --git a/bioxelnodes/assets/Nodes/BioxelNodes_4.0.blend b/bioxelnodes/assets/Nodes/BioxelNodes_4.0.blend new file mode 100644 index 0000000..b938d23 --- /dev/null +++ b/bioxelnodes/assets/Nodes/BioxelNodes_4.0.blend @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:62d5d5bc44343f9bca7d73c6b447661720a5b2de0be4cd5fafeeb204dc32e886 +size 1635596 diff --git a/bioxelnodes/assets/Nodes/BioxelNodes.blend b/bioxelnodes/assets/Nodes/BioxelNodes_4.1.blend similarity index 100% rename from bioxelnodes/assets/Nodes/BioxelNodes.blend rename to bioxelnodes/assets/Nodes/BioxelNodes_4.1.blend diff --git a/bioxelnodes/auto_load.py b/bioxelnodes/auto_load.py index ba6d428..6b4eede 100644 --- a/bioxelnodes/auto_load.py +++ b/bioxelnodes/auto_load.py @@ -16,6 +16,7 @@ modules = None ordered_classes = None + def init(): global modules global ordered_classes @@ -23,6 +24,7 @@ def init(): modules = get_all_submodules(Path(__file__).parent) ordered_classes = get_ordered_classes_to_register(modules) + def register(): for cls in ordered_classes: bpy.utils.register_class(cls) @@ -33,15 +35,22 @@ def register(): if hasattr(module, "register"): module.register() + def unregister(): for cls in reversed(ordered_classes): - bpy.utils.unregister_class(cls) + try: + bpy.utils.unregister_class(cls) + except Exception as e: + print(f"Fail to unregister {cls}, skiped") for module in modules: - if module.__name__ == __name__: - continue - if hasattr(module, "unregister"): - module.unregister() + try: + if module.__name__ == __name__: + continue + if hasattr(module, "unregister"): + module.unregister() + except Exception as e: + print(f"Fail to unregister {module}, skiped") # Import modules @@ -50,10 +59,12 @@ def unregister(): def get_all_submodules(directory): return list(iter_submodules(directory, directory.name)) + def iter_submodules(path, package_name): for name in sorted(iter_submodule_names(path)): yield importlib.import_module("." + name, package_name) + def iter_submodule_names(path, root=""): for _, module_name, is_package in pkgutil.iter_modules([str(path)]): if is_package: @@ -70,19 +81,24 @@ def iter_submodule_names(path, root=""): def get_ordered_classes_to_register(modules): return toposort(get_register_deps_dict(modules)) + def get_register_deps_dict(modules): my_classes = set(iter_my_classes(modules)) - my_classes_by_idname = {cls.bl_idname : cls for cls in my_classes if hasattr(cls, "bl_idname")} + my_classes_by_idname = { + cls.bl_idname: cls for cls in my_classes if hasattr(cls, "bl_idname")} deps_dict = {} for cls in my_classes: - deps_dict[cls] = set(iter_my_register_deps(cls, my_classes, my_classes_by_idname)) + deps_dict[cls] = set(iter_my_register_deps( + cls, my_classes, my_classes_by_idname)) return deps_dict + def iter_my_register_deps(cls, my_classes, my_classes_by_idname): yield from iter_my_deps_from_annotations(cls, my_classes) yield from iter_my_deps_from_parent_id(cls, my_classes_by_idname) + def iter_my_deps_from_annotations(cls, my_classes): for value in typing.get_type_hints(cls, {}, {}).values(): dependency = get_dependency_from_annotation(value) @@ -90,6 +106,7 @@ def iter_my_deps_from_annotations(cls, my_classes): if dependency in my_classes: yield dependency + def get_dependency_from_annotation(value): if blender_version >= (2, 93): if isinstance(value, bpy.props._PropertyDeferred): @@ -100,6 +117,7 @@ def get_dependency_from_annotation(value): return value[1]["type"] return None + def iter_my_deps_from_parent_id(cls, my_classes_by_idname): if bpy.types.Panel in cls.__bases__: parent_idname = getattr(cls, "bl_parent_id", None) @@ -108,6 +126,7 @@ def iter_my_deps_from_parent_id(cls, my_classes_by_idname): if parent_cls is not None: yield parent_cls + def iter_my_classes(modules): base_types = get_register_base_types() for cls in get_classes_in_modules(modules): @@ -115,6 +134,7 @@ def iter_my_classes(modules): if not getattr(cls, "is_registered", False): yield cls + def get_classes_in_modules(modules): classes = set() for module in modules: @@ -122,11 +142,13 @@ def get_classes_in_modules(modules): classes.add(cls) return classes + def iter_classes_in_module(module): for value in module.__dict__.values(): if inspect.isclass(value): yield value + def get_register_base_types(): return set(getattr(bpy.types, name) for name in [ "Panel", "Operator", "PropertyGroup", "FileHandler", @@ -134,7 +156,7 @@ def get_register_base_types(): "Node", "NodeSocket", "NodeTree", "UIList", "RenderEngine", "Gizmo", "GizmoGroup", - ]) + ] if hasattr(bpy.types, name)) # Find order to register to solve dependencies @@ -151,5 +173,6 @@ def toposort(deps_dict): sorted_values.add(value) else: unsorted.append(value) - deps_dict = {value : deps_dict[value] - sorted_values for value in unsorted} + deps_dict = {value: deps_dict[value] - + sorted_values for value in unsorted} return sorted_list diff --git a/bioxelnodes/convert.py b/bioxelnodes/convert.py index d083800..42b3162 100644 --- a/bioxelnodes/convert.py +++ b/bioxelnodes/convert.py @@ -5,7 +5,7 @@ class ConvertToMesh(bpy.types.Operator): bl_idname = "bioxelnodes.convert_to_mesh" bl_label = "Bioxels To Mesh" - bl_description = "Convert Bioxels To Mesh." + bl_description = "Convert Bioxels To Mesh" bl_options = {'UNDO'} @classmethod diff --git a/bioxelnodes/customnodes/__init__.py b/bioxelnodes/customnodes/__init__.py index f809877..bfad98c 100644 --- a/bioxelnodes/customnodes/__init__.py +++ b/bioxelnodes/customnodes/__init__.py @@ -1 +1 @@ -from .menu import CustomNodes \ No newline at end of file +from .menus import CustomNodes \ No newline at end of file diff --git a/bioxelnodes/customnodes/menu.py b/bioxelnodes/customnodes/menus.py similarity index 96% rename from bioxelnodes/customnodes/menu.py rename to bioxelnodes/customnodes/menus.py index 78c0fac..eac702f 100644 --- a/bioxelnodes/customnodes/menu.py +++ b/bioxelnodes/customnodes/menus.py @@ -3,12 +3,6 @@ from pathlib import Path from .nodes import AddCustomNode -bpy.types.Scene.custom_nodes_dir = bpy.props.StringProperty( - name="Nodes Directory", - subtype='DIR_PATH', - default="//" -) - class SaveAllNodes(bpy.types.Operator): bl_idname = "customnodes.save_all_nodes" @@ -182,12 +176,17 @@ def register(self): bpy.utils.register_class(cls) bpy.types.NODE_MT_add.append(self.add_node_menu) + bpy.types.Scene.custom_nodes_dir = bpy.props.StringProperty( + name="Nodes Directory", + subtype='DIR_PATH', + default="//" + ) def unregister(self): + bpy.types.NODE_MT_add.remove(self.add_node_menu) try: for cls in reversed(self.menu_classes): bpy.utils.unregister_class(cls) - bpy.types.NODE_MT_add.remove(self.add_node_menu) except RuntimeError: pass diff --git a/bioxelnodes/externalpackage/__init__.py b/bioxelnodes/externalpackage/__init__.py index c00e7fb..a46ad0f 100644 --- a/bioxelnodes/externalpackage/__init__.py +++ b/bioxelnodes/externalpackage/__init__.py @@ -1 +1,2 @@ -from .preferences import ExternalPackagePreferences \ No newline at end of file +from .preferences import ExternalPackagePreferences +from .package import PackageInstaller diff --git a/bioxelnodes/externalpackage/package.py b/bioxelnodes/externalpackage/package.py index c55ba62..368a32c 100644 --- a/bioxelnodes/externalpackage/package.py +++ b/bioxelnodes/externalpackage/package.py @@ -42,12 +42,13 @@ def __init__(self, package_name, error_message): class PackageInstaller(): def __init__( self, - log_dir: str, requirements_dir: str, + log_dir: str = None, pypi_mirror_provider='Default', ) -> None: self.pypi_mirror_provider = pypi_mirror_provider - self.log_path: Path = Path(log_dir) + self.log_path: Path = Path(log_dir) if log_dir \ + else Path.home() / '.externalpackage' / 'logs' self.requirements_path: Path = Path(requirements_dir) def start_logging(self, logfile_name: str = 'side-packages-install') -> logging.Logger: @@ -250,7 +251,7 @@ def run_python(self, cmd_list: list = None, timeout: int = 600): if result.returncode != 0: log.error('Command failed: %s', cmd_list) log.error('stdout: %s', result.stdout.decode()) - log.error('stderr: %s', result.stderr.decode()) + log.error('stderr: %s', result.stderr.decode(errors='ignore')) else: log.info('Command succeeded: %s', cmd_list) log.info('stdout: %s', result.stdout.decode()) @@ -350,6 +351,7 @@ class EXTERNALPACKAGE_OT_Install_Package(bpy.types.Operator): name='Python Package', description='Python Package to Install' ) # type: ignore + version: bpy.props.StringProperty( name='Python Package', description='Python Package to Install' diff --git a/bioxelnodes/externalpackage/preferences.py b/bioxelnodes/externalpackage/preferences.py index 3c99fed..f15aff8 100644 --- a/bioxelnodes/externalpackage/preferences.py +++ b/bioxelnodes/externalpackage/preferences.py @@ -1,4 +1,5 @@ import bpy +import subprocess from pathlib import Path from .package import PackageInstaller, PYPI_MIRROR @@ -10,6 +11,25 @@ def get_pypi_mirrors(self, context, edit_text): return PYPI_MIRROR.keys() +class RebootBlender(bpy.types.Operator): + bl_idname = "externalpackage.reboot_blender" + bl_label = "Reboot Blender" + bl_description = "Reboot Blender" + bl_options = {'UNDO'} + + def invoke(self, context, event): + context.window_manager.invoke_confirm(self, event) + return {'RUNNING_MODAL'} + + def execute(self, context): + blender_launcher = Path( + bpy.app.binary_path).parent / "blender-launcher.exe" + subprocess.run([str(blender_launcher), "-con", "--python-expr", + "import bpy; bpy.ops.wm.recover_last_session()"]) + bpy.ops.wm.quit_blender() + return {'FINISHED'} + + class ExternalPackagePreferences(): requirements_dir: bpy.props.StringProperty( name="requirements.txt Directory", @@ -34,11 +54,12 @@ class ExternalPackagePreferences(): def draw(self, context): layout = self.layout - layout.label(text="Install the required packages.") + layout.label( + text='**Install the required packages, then hit "Reboot Blender"**') col_main = layout.column(heading='', align=False) row_import = col_main.row() - row_import.prop(self, 'pypi_mirror_provider', text='Set PyPI Mirror') + row_import.prop(self, 'pypi_mirror_provider', text='PyPI Mirror') installer = PackageInstaller( pypi_mirror_provider=self.pypi_mirror_provider, @@ -70,3 +91,5 @@ def draw(self, context): op.package = name op.version = version op.description = f'Install required python package: {name}' + + layout.operator(RebootBlender.bl_idname) diff --git a/bioxelnodes/io.py b/bioxelnodes/io.py index e93a7de..3285caa 100644 --- a/bioxelnodes/io.py +++ b/bioxelnodes/io.py @@ -6,71 +6,144 @@ from pathlib import Path from uuid import uuid4 import mathutils -from .utils import calc_bbox_verts, extract_last_number, get_bioxels_obj, get_node_by_type, show_message +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 +try: + import SimpleITK as sitk +except: + ... + +SUPPORT_EXTS = ['.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', '.DICOM', + '.bmp', '.BMP', + '.jpg', '.JPG', '.jpeg', '.JPEG', + '.tif', '.TIF', '.tiff', '.TIFF', + '.png', '.PNG'] + +DICOM_EXTS = ['.dcm', '.DICOM'] + +FH_EXTS = ['.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_bioxels_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_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 -SUPPORT_EXTS = ['.dcm', '.tif', '.tiff', '.png', '.bmp', '', '.jpg'] - - -def get_data_files(filepath: str): - file_path = Path(filepath).resolve() - suffix = file_path.suffix - - files = list(file_path.parent.iterdir()) - files = [f for f in files if f.is_file() and f.suffix == suffix] - def last_number(file: Path): - return extract_last_number(file.stem) +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) - files.sort(key=last_number) - files = [str(f) for f in files] - return files +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 on_orig_spacing_changed(self, context): - if self.auto: - self.auto = False - new_orig_spacing = tuple(self.orig_spacing) - orig_shape = tuple(self.orig_shape) - bioxel_size = float(self.bioxel_size) +def collect_image_sequence(filepath: str): + file_path = Path(filepath).resolve() - self.bioxels_shape = ( - int(orig_shape[0] / bioxel_size * new_orig_spacing[0]), - int(orig_shape[1] / bioxel_size * new_orig_spacing[1]), - int(orig_shape[2] / bioxel_size * new_orig_spacing[2]), - ) + 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 read_image(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) + image = reader.Execute() + name = dir_path.name + + elif ext in SEQUENCE_EXTS: + image = sitk.ReadImage(filepath) + if image.GetDimension() == 2: + sequence = collect_image_sequence(filepath) + image = sitk.ReadImage(sequence) + name = get_sequence_name(filepath) + else: + image = sitk.ReadImage(filepath) + name = Path(filepath).name.removesuffix(ext) else: - self.auto = True - + image = sitk.ReadImage(filepath) + name = Path(filepath).name.removesuffix(ext) -def on_bioxel_size_changed(self, context): - if self.auto: - self.auto = False - new_bioxel_size = float(self.bioxel_size) + return image, name - orig_shape = tuple(self.orig_shape) - orig_spacing = tuple(self.orig_spacing) - - self.bioxels_shape = ( - int(orig_shape[0] / new_bioxel_size * orig_spacing[0]), - int(orig_shape[1] / new_bioxel_size * orig_spacing[1]), - int(orig_shape[2] / new_bioxel_size * orig_spacing[2]), - ) - else: - self.auto = True +def rgb2gray(image): + # Convert sRGB image to gray scale and rescale results to [0,255] + channels = [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]) -def on_info_changed(self, context): - for region in context.area.regions: - if region.type == "UI": - region.tag_redraw() + return sitk.Cast(I, sitk.sitkFloat32) -class ImportDICOMDialog(bpy.types.Operator): - bl_idname = "bioxelnodes.import_dicom_dialog" +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_description = "Import Volume Data as Bioxels (VDB)" bl_options = {'UNDO'} filepath: bpy.props.StringProperty( @@ -78,64 +151,67 @@ class ImportDICOMDialog(bpy.types.Operator): options={'HIDDEN'} ) # type: ignore - bioxels_shape: bpy.props.IntVectorProperty( - name="Bioxels Shape (ReadOnly)", - min=0, - default=(100, 100, 100) + series_id: bpy.props.StringProperty() # type: ignore + + resample_method: bpy.props.EnumProperty( + name="Resample Method", + default="linear", + items=[("linear", "Linear", ""), + ("nearest_neighbor", "Nearest Neighbor", ""), + ("gaussian", "Gaussian", "")] + ) # type: ignore + + read_as: bpy.props.EnumProperty( + name="Read as", + default="scalar", + items=[("scalar", "Scalar", ""), + ("labels", "Labels", "")] + ) # type: ignore + + label_index: bpy.props.IntProperty( + name="Label Index", + default=1 ) # type: ignore bioxel_size: bpy.props.FloatProperty( - name="Bioxel Size", + name="Bioxel Size (Larger size means small resolution)", soft_min=0.1, soft_max=10.0, min=1e-2, max=1e2, default=1, - update=on_bioxel_size_changed ) # type: ignore orig_spacing: bpy.props.FloatVectorProperty( name="Original Spacing", default=(1, 1, 1), - update=on_orig_spacing_changed ) # type: ignore orig_shape: bpy.props.IntVectorProperty( name="Original Shape", - default=(100, 100, 100), - options={'HIDDEN'} - ) # type: ignore - - auto: bpy.props.BoolProperty( - name="Auto Setting", - default=False, - options={'HIDDEN'} + default=(100, 100, 100) ) # type: ignore scene_scale: bpy.props.FloatProperty( - name="Scene Scale", + name="Scene Scale (Bioxels Unit pre Blender Unit)", soft_min=0.001, soft_max=100.0, min=1e-6, max=1e6, default=0.01, ) # type: ignore - do_add_segmentnode: bpy.props.BoolProperty( - name="Add Segment Node", + do_orient: bpy.props.BoolProperty( + name="Orient to RAS", default=True, ) # type: ignore - do_change_render_setting: bpy.props.BoolProperty( - name="Change Render Setting", - default=True, + invert_scalar: bpy.props.BoolProperty( + name="Invert Scalar (Background value maybe higher than object)", + default=False, ) # type: ignore def execute(self, context): - files = get_data_files(self.filepath) - name = Path(self.filepath).parent.name - - import SimpleITK as sitk - image = sitk.ReadImage(files) + image, bioxels_name = read_image(self.filepath, self.series_id) - bioxel_size = float(self.bioxel_size) - orig_spacing = tuple(self.orig_spacing) + bioxel_size = self.bioxel_size + orig_spacing = self.orig_spacing image_spacing = image.GetSpacing() image_shape = image.GetSize() @@ -145,32 +221,51 @@ def execute(self, context): image_spacing[2] / orig_spacing[2] * bioxel_size ) - bioxels_shape = ( - int(image_shape[0] / bioxel_size * orig_spacing[0]), - int(image_shape[1] / bioxel_size * orig_spacing[1]), - int(image_shape[2] / bioxel_size * orig_spacing[2]), - ) - - print("Resampling...") + bioxels_shape = get_bioxels_shape( + bioxel_size, image_shape, orig_spacing) + + if self.read_as == "labels": + image = sitk.Cast(image, sitk.sitkUInt16) + default_value = 0 + elif self.read_as == "scalar": + if "vector" in image.GetPixelIDTypeAsString(): + print("Convet to Grayscale...") + image = rgb2gray(image) + else: + image = sitk.Cast(image, sitk.sitkFloat32) + + stats = sitk.StatisticsImageFilter() + stats.Execute(image) + default_value = stats.GetMaximum() if self.invert_scalar else stats.GetMinimum() + + if self.resample_method == "linear": + interpolator = sitk.sitkLinear + elif self.resample_method == "nearest_neighbor": + interpolator = sitk.sitkNearestNeighbor + elif self.resample_method == "gaussian": + interpolator = sitk.sitkGaussian + + print(f"Resampling...") image = sitk.Resample( image1=image, size=bioxels_shape, transform=sitk.Transform(), - interpolator=sitk.sitkLinear, + interpolator=interpolator, outputOrigin=image.GetOrigin(), outputSpacing=bioxels_spacing, outputDirection=image.GetDirection(), - defaultPixelValue=0, + defaultPixelValue=default_value, outputPixelType=image.GetPixelID(), ) - print("Orienting to RAS...") - image = sitk.DICOMOrient(image, 'RAS') + if self.do_orient: + print("Orienting to RAS...") + image = sitk.DICOMOrient(image, 'RAS') - array = sitk.GetArrayFromImage(image) - orig_dtype = str(array.dtype) - print(f"Coverting Dtype from {orig_dtype} to float...") - array = array.astype(float) + print("Oriented Origin:", image.GetOrigin()) + print("Oriented Direction:", image.GetDirection()) + + # return {'FINISHED'} # ITK indices, by convention, are [i,j,k] while NumPy indices are [k,j,i] # https://www.slicer.org/wiki/Coordinate_systems @@ -179,27 +274,63 @@ def execute(self, context): # R (ight) i -> k -> x # A (nterior) j -> j -> y # S (uperior) k -> i -> z + array = sitk.GetArrayFromImage(image) - array = np.transpose(array) - bioxels_max = float(np.max(array)) - bioxels_min = float(np.min(array)) - bioxels_shape = array.shape + 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] - print("Bioxel Size:", bioxel_size) - print("Bioxels Shape:", bioxels_shape) + array = np.transpose(array) + bioxels_shape = array.shape bioxels_offset = 0.0 - if bioxels_min < 0 and orig_dtype[0] != "u": - bioxels_offset = -bioxels_min - array = array + np.full_like(array, bioxels_offset) + + 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)) - print("Offseted Max:", bioxels_max) - print("Offseted Min:", bioxels_min) - # Build VDB - grid = vdb.FloatGrid() - grid.copyFromArray(array.copy()) + 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 @@ -210,22 +341,26 @@ def execute(self, context): to_up='Y' ).to_4x4() + origin = image.GetOrigin() + direction = image.GetDirection() + mat_location = mathutils.Matrix.Translation( - mathutils.Vector(image.GetOrigin()) + mathutils.Vector(origin) ) mat_rotation = mathutils.Matrix( - np.array(image.GetDirection()).reshape((3, 3)) + np.array(direction).reshape((3, 3)) ).to_4x4() mat_scale = mathutils.Matrix.Scale( bioxel_size, 4 ) - transfrom = mat_lps2ras @ mat_location @ mat_rotation @ mat_scale + 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 = "value" + grid.name = "scalar" preferences = context.preferences.addons[__package__].preferences vdb_dirpath = Path(preferences.cache_dir, 'VDBs') @@ -243,8 +378,8 @@ def execute(self, context): bioxels_obj = bpy.context.active_object # Set props to VDB object - bioxels_obj.name = f"{name}_Bioxels" - bioxels_obj.data.name = f"{name}_Bioxels" + bioxels_obj.name = f"{bioxels_name}_Bioxels" + bioxels_obj.data.name = f"{bioxels_name}_Bioxels" # Make transformation scene_scale = float(self.scene_scale) @@ -289,8 +424,8 @@ def execute(self, context): vert.co = bbox_transform @ mathutils.Vector(bbox_verts[index]) bioxels_obj.parent = container_obj - container_obj.name = name - container_obj.data.name = name + 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 @@ -315,7 +450,7 @@ def execute(self, context): # Create BioxelNodes to VDB object print(f"Creating BioxelNodes to the VDB...") - if self.do_add_segmentnode: + if preferences.do_add_segmentnode: nodes = node_tree.nodes links = node_tree.links @@ -324,11 +459,14 @@ def execute(self, context): segment_node = custom_nodes.add_node( nodes, 'BioxelNodes_Segment') + + segment_node.inputs['Threshold'].default_value = bioxels_default_threshold + links.new(input_node.outputs[0], segment_node.inputs[0]) links.new(segment_node.outputs[0], output_node.inputs[0]) # Change render setting for better result - if self.do_change_render_setting: + 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 @@ -338,49 +476,98 @@ def execute(self, context): return {'FINISHED'} def invoke(self, context, event): - # print(tuple(self.orig_shape)) - self.auto = True - self.bioxel_size = 1 - context.window_manager.invoke_props_dialog(self) + 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_description = "Import Volume Data as Bioxels (VDB)" bl_options = {'UNDO'} - filepath: bpy.props.StringProperty( - subtype="FILE_PATH" - ) # type: ignore + filepath: bpy.props.StringProperty(subtype="FILE_PATH") # type: ignore + directory: bpy.props.StringProperty(subtype='DIR_PATH') # type: ignore - ok: bpy.props.BoolProperty( - default=True + 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): - if Path(self.filepath).suffix not in SUPPORT_EXTS: - self.report({"WARNING"}, "Not Supported extension.") + ext = get_ext(self.filepath) + if ext not in SUPPORT_EXTS: + self.report({"WARNING"}, "Not supported extension.") return {'CANCELLED'} - files = get_data_files(self.filepath) - - import SimpleITK as sitk + 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())] - image = sitk.ReadImage(files) + print("Meta Data:") + for stats in stats_table: + print("| {: >10} | {: >40} |".format(*stats)) - print("Collecting Meta Data...") - print("Original Shape:", image.GetSize()) - print("Original Spacing:", image.GetSpacing()) - print("Original Origin:", image.GetOrigin()) - print("Original Direction:", image.GetDirection()) + do_orient = ext not in SEQUENCE_EXTS or ext in DICOM_EXTS - bpy.ops.bioxelnodes.import_dicom_dialog( + bpy.ops.bioxelnodes.import_volume_data_dialog( 'INVOKE_DEFAULT', filepath=self.filepath, orig_shape=image.GetSize(), - orig_spacing=image.GetSpacing() + orig_spacing=image.GetSpacing(), + series_id=self.series_id or "", + do_orient=do_orient ) self.report({"INFO"}, "Successfully Readed.") @@ -392,29 +579,56 @@ def modal(self, context, event): return {'FINISHED'} def invoke(self, context, event): - if not self.filepath: + if not self.filepath and not self.directory: return {'CANCELLED'} - show_message('Reading image data, it may take a while', + 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 ImportDICOM(bpy.types.Operator): - bl_idname = "bioxelnodes.import_dicom" + +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_description = "Import Volume Data as Bioxels (VDB)" bl_options = {'UNDO'} - filepath: bpy.props.StringProperty( - subtype="FILE_PATH" - ) # type: ignore + 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 + filepath=self.filepath, + directory=self.directory ) return {'FINISHED'} @@ -423,21 +637,24 @@ def invoke(self, context, event): return {'RUNNING_MODAL'} -class BIOXELNODES_FH_ImportDicom(bpy.types.FileHandler): - bl_idname = "BIOXELNODES_FH_ImportDicom" - bl_label = "File handler for dicom import" - bl_import_operator = "bioxelnodes.read_dicom" - bl_file_extensions = ".dcm" +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') + @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_description = "Export Bioxels original VDB data" bl_options = {'UNDO'} filepath: bpy.props.StringProperty( diff --git a/bioxelnodes/io_points.py b/bioxelnodes/io_points.py new file mode 100644 index 0000000..083fdf8 --- /dev/null +++ b/bioxelnodes/io_points.py @@ -0,0 +1,221 @@ +# TODO: WIP +import bpy +import bmesh + + +def create_points_obj(points, name="points"): + bpy.ops.mesh.primitive_cube_add( + enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1) + ) + obj = bpy.context.active_object + mesh = obj.data + + bm = bmesh.new() + value_layer = bm.verts.layers.float.new('value') + + for point in points: + pos = point['pos'] + value = point['value'] + vert = bm.verts.new(pos) # add a new vert + vert[value_layer] = value + + # make the bmesh the object's mesh + bm.to_mesh(mesh) + bm.free() # always do this when finished + return obj + + +# class ImportDICOMPointsDialog(bpy.types.Operator): +# bl_idname = "bioxelnodes.import_dicom_points_dialog" +# bl_label = "Volume Data as Bioxels" +# bl_description = "Import Volume Data as Bioxels (VDB)" +# bl_options = {'UNDO'} + +# filepath: bpy.props.StringProperty( +# subtype="FILE_PATH", +# options={'HIDDEN'} +# ) # type: ignore + +# bioxels_shape: bpy.props.IntVectorProperty( +# name="Bioxels Shape (ReadOnly)", +# min=0, +# default=(100, 100, 100) +# ) # type: ignore + +# bioxel_size: bpy.props.FloatProperty( +# name="Bioxel Size", +# soft_min=0.1, soft_max=10.0, +# min=1e-2, max=1e2, +# default=1, +# update=on_bioxel_size_changed +# ) # type: ignore + +# orig_spacing: bpy.props.FloatVectorProperty( +# name="Original Spacing", +# default=(1, 1, 1), +# update=on_orig_spacing_changed +# ) # type: ignore + +# orig_shape: bpy.props.IntVectorProperty( +# name="Original Shape", +# default=(100, 100, 100), +# options={'HIDDEN'} +# ) # type: ignore + +# auto: bpy.props.BoolProperty( +# name="Auto Setting", +# default=False, +# options={'HIDDEN'} +# ) # type: ignore + +# scene_scale: bpy.props.FloatProperty( +# name="Scene Scale", +# soft_min=0.001, soft_max=100.0, +# min=1e-6, max=1e6, +# default=0.01, +# ) # 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, +# ) # type: ignore + +# def execute(self, context): +# files = get_data_files(self.filepath) +# name = Path(self.filepath).parent.name + +# image = sitk.ReadImage(files) + +# bioxel_size = float(self.bioxel_size) +# orig_spacing = tuple(self.orig_spacing) +# image_spacing = image.GetSpacing() +# image_shape = image.GetSize() + +# bioxels_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 = ( +# int(image_shape[0] / bioxel_size * orig_spacing[0]), +# int(image_shape[1] / bioxel_size * orig_spacing[1]), +# int(image_shape[2] / bioxel_size * orig_spacing[2]), +# ) + +# print("Resampling...") +# image = sitk.Resample( +# image1=image, +# size=bioxels_shape, +# transform=sitk.Transform(), +# interpolator=sitk.sitkLinear, +# outputOrigin=image.GetOrigin(), +# outputSpacing=bioxels_spacing, +# outputDirection=image.GetDirection(), +# defaultPixelValue=0, +# outputPixelType=image.GetPixelID(), +# ) + +# print("Orienting to RAS...") +# image = sitk.DICOMOrient(image, 'RAS') + +# array = sitk.GetArrayFromImage(image) +# orig_dtype = str(array.dtype) +# print(f"Coverting Dtype from {orig_dtype} to float...") +# array = array.astype(float) + +# # ITK indices, by convention, are [i,j,k] while NumPy indices are [k,j,i] +# # https://www.slicer.org/wiki/Coordinate_systems + +# # ITK Numpy 3D +# # R (ight) i -> k -> x +# # A (nterior) j -> j -> y +# # S (uperior) k -> i -> z + +# array = np.transpose(array) +# bioxels_max = float(np.max(array)) +# bioxels_min = float(np.min(array)) +# bioxels_shape = array.shape + +# print("Bioxel Size:", bioxel_size) +# print("Bioxels Shape:", bioxels_shape) + +# bioxels_offset = 0.0 +# if bioxels_min < 0 and orig_dtype[0] != "u": +# bioxels_offset = -bioxels_min +# array = array + np.full_like(array, bioxels_offset) +# bioxels_max = float(np.max(array)) +# bioxels_min = float(np.min(array)) +# print("Offseted Max:", bioxels_max) +# print("Offseted Min:", bioxels_min) + +# points = [] +# for x in range(array.shape[0]): +# for y in range(array.shape[1]): +# for z in range(array.shape[2]): +# points.append({ +# "pos": (x, y, z), +# "value": array[x, y, z], +# }) + +# # # Build VDB +# # grid = vdb.FloatGrid() +# # grid.copyFromArray(array.copy()) + +# # # 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(image.GetOrigin()) +# # ) + +# # mat_rotation = mathutils.Matrix( +# # np.array(image.GetDirection()).reshape((3, 3)) +# # ).to_4x4() + +# # mat_scale = mathutils.Matrix.Scale( +# # bioxel_size, 4 +# # ) + +# # transfrom = mat_lps2ras @ mat_location @ mat_rotation @ mat_scale + +# obj = create_points_obj(points) + +# # 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 +# ) + +# obj.matrix_world = mat_ras2blender @ mat_scene_scale + +# self.report({"INFO"}, "Successfully Imported") + +# return {'FINISHED'} + +# def invoke(self, context, event): +# # print(tuple(self.orig_shape)) +# self.auto = True +# self.bioxel_size = 1 +# context.window_manager.invoke_props_dialog(self) +# return {'RUNNING_MODAL'} diff --git a/bioxelnodes/menu.py b/bioxelnodes/menus.py similarity index 86% rename from bioxelnodes/menu.py rename to bioxelnodes/menus.py index 930a53a..82d3c65 100644 --- a/bioxelnodes/menu.py +++ b/bioxelnodes/menus.py @@ -1,7 +1,7 @@ -from bioxelnodes.misc import SaveBioxels import bpy from .convert import ConvertToMesh -from .io import ExportVDB, ImportDICOM +from .io import ExportVDB, ImportVolumeData +from .misc import SaveBioxels class ObjectMenu(bpy.types.Menu): @@ -10,15 +10,15 @@ class ObjectMenu(bpy.types.Menu): def draw(self, context): layout = self.layout - layout.operator(SaveBioxels.bl_idname) - layout.separator() layout.operator(ConvertToMesh.bl_idname) + layout.separator() + layout.operator(SaveBioxels.bl_idname) def TOPBAR_FILE_IMPORT(self, context): layout = self.layout layout.separator() - layout.operator(ImportDICOM.bl_idname) + layout.operator(ImportVolumeData.bl_idname) def TOPBAR_FILE_EXPORT(self, context): @@ -30,17 +30,16 @@ def TOPBAR_FILE_EXPORT(self, context): def VIEW3D_OBJECT(self, context): layout = self.layout layout.menu(ObjectMenu.bl_idname) - layout.separator() -def create_menu(): +def add(): bpy.types.TOPBAR_MT_file_import.append(TOPBAR_FILE_IMPORT) bpy.types.TOPBAR_MT_file_export.append(TOPBAR_FILE_EXPORT) bpy.types.VIEW3D_MT_object_context_menu.prepend(VIEW3D_OBJECT) -def remove_menu(): +def remove(): bpy.types.TOPBAR_MT_file_import.remove(TOPBAR_FILE_IMPORT) bpy.types.TOPBAR_MT_file_export.remove(TOPBAR_FILE_EXPORT) bpy.types.VIEW3D_MT_object_context_menu.remove(VIEW3D_OBJECT) diff --git a/bioxelnodes/misc.py b/bioxelnodes/misc.py index 56d3bfc..5ef4b00 100644 --- a/bioxelnodes/misc.py +++ b/bioxelnodes/misc.py @@ -1,7 +1,7 @@ +import bpy from pathlib import Path import shutil from bioxelnodes.utils import get_all_bioxels_objs, get_bioxels_obj -import bpy class SaveBioxels(bpy.types.Operator): diff --git a/bioxelnodes/nodes.py b/bioxelnodes/nodes.py index 51edcca..74729f2 100644 --- a/bioxelnodes/nodes.py +++ b/bioxelnodes/nodes.py @@ -40,7 +40,7 @@ def set_prop_to_node_factory(source_prop, target_prop): MENU_ITEMS = [ { - 'label': 'Present', + 'label': 'Presets', 'icon': 'MESH_MONKEY', 'items': [ { @@ -52,17 +52,17 @@ def set_prop_to_node_factory(source_prop, target_prop): 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': '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"), + # ]) + # } ] }, { @@ -71,7 +71,7 @@ def set_prop_to_node_factory(source_prop, target_prop): 'items': [ { 'label': 'Segment by Level', - 'icon': 'AREA_JOIN', + 'icon': 'EMPTY_SINGLE_ARROW', 'node_type': 'BioxelNodes_SegmentByLevel', 'node_description': '', 'node_callback': "\n".join([ @@ -81,24 +81,24 @@ def set_prop_to_node_factory(source_prop, target_prop): }, { 'label': 'Segment by Range', - 'icon': 'AREA_SWAP', + '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': 'OUTLINER_OB_FORCE_FIELD', - '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': '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"), + # ]) + # } ] }, { @@ -112,8 +112,13 @@ def set_prop_to_node_factory(source_prop, target_prop): 'node_description': '' } ] - }, - { + } +] + +NODE_FILE = "BioxelNodes_4.0" + +if bpy.app.version >= (4, 1, 0): + MENU_ITEMS.append({ 'label': 'Slicer', 'icon': 'CLIPUV_DEHLT', 'items': [ @@ -136,12 +141,21 @@ def set_prop_to_node_factory(source_prop, target_prop): 'node_description': '', } ] - }, -] + }) + NODE_FILE = "BioxelNodes_4.1" + custom_nodes = CustomNodes( menu_items=MENU_ITEMS, - nodes_file=Path(__file__).parent/"assets/Nodes/BioxelNodes.blend", + nodes_file=Path(__file__).parent / f"assets/Nodes/{NODE_FILE}.blend", root_label='Bioxel Nodes', root_icon="FILE_VOLUME", ) + + +def register(): + custom_nodes.register() + + +def unregister(): + custom_nodes.unregister() diff --git a/bioxelnodes/preferences.py b/bioxelnodes/preferences.py index bb1036d..7972589 100644 --- a/bioxelnodes/preferences.py +++ b/bioxelnodes/preferences.py @@ -7,16 +7,30 @@ class BioxelNodesPreferences(bpy.types.AddonPreferences, ExternalPackagePreferen bl_idname = __package__ cache_dir: bpy.props.StringProperty( - name="VDB Cache Directory", + name="Set Cache Directory", subtype='DIR_PATH', 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, + ) # type: ignore + def draw(self, context): layout = self.layout - layout.label(text="Configuration") - layout.prop(self, 'cache_dir', text='Set Cache Directory') # ExternalPackagePreferences Config self.requirements_dir = str(Path(__file__).parent) super().draw(context) + + layout.label(text="Configuration") + layout.prop(self, 'cache_dir') + + layout.prop(self, "do_change_render_setting") + layout.prop(self, "do_add_segmentnode") diff --git a/bioxelnodes/props.py b/bioxelnodes/props.py new file mode 100644 index 0000000..d46bfd6 --- /dev/null +++ b/bioxelnodes/props.py @@ -0,0 +1,5 @@ +import bpy + +class BIOXELNODES_Series(bpy.types.PropertyGroup): + id: bpy.props.StringProperty() # type: ignore + label: bpy.props.StringProperty() # type: ignore diff --git a/bioxelnodes/utils.py b/bioxelnodes/utils.py index b00b070..cbd5d0d 100644 --- a/bioxelnodes/utils.py +++ b/bioxelnodes/utils.py @@ -2,9 +2,12 @@ import mathutils -def get_node_by_type(nodes, type_name: str): - return [node for node in nodes if type(node).__name__ == type_name] +def get_type(cls): + return type(cls).__name__ + +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'): @@ -81,6 +84,7 @@ def get_bioxels_obj(current_obj): return bioxels_obj + def get_all_bioxels_objs(): bioxels_objs = [] @@ -88,10 +92,11 @@ def get_all_bioxels_objs(): if obj.parent: if obj.parent.get('bioxels_container') and obj.get('bioxels'): bioxels_objs.append(obj) - + return list(set(bioxels_objs)) -def extract_last_number(text): + +def get_text_index_str(text): # Initialize an empty string to store the digits digits = "" @@ -110,7 +115,7 @@ def extract_last_number(text): # Reverse the digits string to get the correct order last_number = digits[::-1] - return int(last_number) + return last_number def add_driver(target_prop, var_sources, expression): diff --git a/docs/images/bake_node.png b/docs/assets/bake_node.png similarity index 100% rename from docs/images/bake_node.png rename to docs/assets/bake_node.png diff --git a/docs/images/dependency.png b/docs/assets/dependency.png similarity index 100% rename from docs/images/dependency.png rename to docs/assets/dependency.png diff --git a/docs/images/gallery.png b/docs/assets/gallery.png similarity index 100% rename from docs/images/gallery.png rename to docs/assets/gallery.png diff --git a/docs/images/general_graph.png b/docs/assets/general_graph.png similarity index 100% rename from docs/images/general_graph.png rename to docs/assets/general_graph.png diff --git a/docs/images/general_graph_example.png b/docs/assets/general_graph_example.png similarity index 100% rename from docs/images/general_graph_example.png rename to docs/assets/general_graph_example.png diff --git a/docs/images/import_dialog.png b/docs/assets/import_dialog.png similarity index 100% rename from docs/images/import_dialog.png rename to docs/assets/import_dialog.png diff --git a/docs/images/importing.png b/docs/assets/importing.png similarity index 100% rename from docs/images/importing.png rename to docs/assets/importing.png diff --git a/docs/assets/logo.png b/docs/assets/logo.png new file mode 100644 index 0000000..73e77b4 Binary files /dev/null and b/docs/assets/logo.png differ diff --git a/docs/images/result.png b/docs/assets/result.png similarity index 100% rename from docs/images/result.png rename to docs/assets/result.png diff --git a/docs/images/segment_node.png b/docs/assets/segment_node.png similarity index 100% rename from docs/images/segment_node.png rename to docs/assets/segment_node.png diff --git a/docs/features.md b/docs/features.md new file mode 100644 index 0000000..bacd61f --- /dev/null +++ b/docs/features.md @@ -0,0 +1,5 @@ +# Import Volume Data + +# Convert to Mesh + +# Export Volume Data diff --git a/docs/getting-started.md b/docs/getting-started.md new file mode 100644 index 0000000..34606ed --- /dev/null +++ b/docs/getting-started.md @@ -0,0 +1,60 @@ +# Getting Started + +Currently only support Blender 4.0 or above, make sure you have the correct version of Blender. + +### Add-on Installation + +Download the latest version https://github.com/OmooLab/BioxelNodes/releases/latest +In Blender, `Edit - Preferences - Add-ons - Install`, select the `BioxelNodes_{version}.zip` you just downloaded. + +### Dependency Installation + +The add-on requires a third-party python dependency called SimpleITK, click the Install SimpleITK button below to install the dependency. After clicking, blender may get stuck, it is downloading and installing, just wait for a moment. After the Installation, **restart blender once**. + +![dependency](assets/dependency.png) + +This step may have failed due to network factors, just click "Set PyPI Mirror" to change the mirror. + +### Basic Usage + +First you need to have your volumetric data ready. If not, you can access open research data from [Dryad](https://datadryad.org) (Dryad publishes data exclusively under a [Creative Commons Public Domain License](https://creativecommons.org/public-domain/cc0/)) + +Note: Make sure one folder contains only one sequence, multiple sequences need to be manually split into different folders first. + +In Blender, `File - Import - Volume Data as Bioxels`, select **one** of the .dcm files and click on "Volume Data as Bioxels" (you can also drag one of the .dcm files directly into the 3D viewport to trigger the import, but this is limited to .dcm format files) + +![importing](assets/importing.png) + +It may take a while to read data. After finishing reading, it will pop up a dialog box + +![import dialog](assets/import_dialog.png) + +Ignore the options, just click OK! + +After importing, the necessary nodes are automatically added, the reconstruction and shader are created, and then turned on the cycles rendering to directly see the result. + +![result](assets/result.png) + +Click select Bioxels Object, and open the Geometry Nodes panel to see the following node graph: + +![segment node](assets/segment_node.png) + +You can change the "Threshold" to modify the reconstruction model, or change the "Color", "Density" to modify the shader effect. All the parameters are straightforward, you can understand them by changing the values. + +The node, that named "Segment", is a preset node that combines the steps of 3D reconstruction process and shading process. In general, you need to add one of the segmentation node to reconstruction first, and followed by one of the shader node to set the shader. As you can see in the following figure: + +![general graph](assets/general_graph.png) + +Currently there are 3 types of nodes + +- Segmentation nodes, responsible for splitting the volume into a reconstructed model (we call them "Segment"). +- Shader nodes, responsible for giving shader to the Segment. +- Slicer nodes, responsible for partially cutting the Segment. + +For example: + +![general graph example](assets/general_graph_example.png) + +You can add a "Bake" node between segmentation node and shader node, if the reconstruction process consumes too much computing time. But be sure, you are selecting the volume object, not the container object. + +![bake node](assets/bake_node.png) diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..2c01e8c --- /dev/null +++ b/docs/index.md @@ -0,0 +1,45 @@ +[中文文档](https://uj6xfhbzp0.feishu.cn/wiki/Qx3VwHuNPimeI8kr6nDcvl1DnHf?from=from_copylink) + +# Bioxel Nodes + +![Static Badge](https://img.shields.io/badge/Blender-orange?style=for-the-badge&logo=blender&logoColor=white) +![GitHub License](https://img.shields.io/github/license/OmooLab/BioxelNodes?style=for-the-badge) +![GitHub Release](https://img.shields.io/github/v/release/OmooLab/BioxelNodes?style=for-the-badge) +![GitHub Repo stars](https://img.shields.io/github/stars/OmooLab/BioxelNodes?style=for-the-badge) + +Bioxel Nodes is a Blender add-on for scientific volumetric data visualization. It using Blender's powerful Geometry Nodes | Cycles to process and render volumetric data. + +# About + +Before us, there have been many tutorials and add-ons for importing volumetric data into Blender. However, we found that there were many details that were not addressed in place, some scientific facts were ignored, and the volume rendering was not pretty enough. With Bioxel Nodes, you can easily import the volumetric data into Blender, and more importantly, it can quickly make a beautiful realistic rendering of it. + +Below are some examples with Bioxel Nodes. Thanks to Cycles Render, the volumetric data can be rendered with great detail: + +![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) + +# Supported Format + +| Format | EXT | Test | +| ------ | ---------------------------------------- | ------- | +| DICOM | .dcm, .DICOM | ✅ pass | +| BMP | .bmp, .BMP | ✅ pass | +| JPEG | .jpg, .JPG, .jpeg, .JPEG | ✅ pass | +| PNG | .png, .PNG | ✅ pass | +| TIFF | .tif, .TIF, .tiff, .TIFF | ✅ pass | +| Nifti | .nia, .nii, .nii.gz, .hdr, .img, .img.gz | ✅ pass | +| Nrrd | .nrrd, .nhdr | ✅ pass | +| Meta | .mha, .mhd | yet | +| HDF5 | .hdf, .h4, .hdf4, .he2, .h5, .hdf5, .he5 | ✅ pass | +| VTK | .vtk | yet | +| BioRad | .PIC, .pic | yet | +| Gipl | .gipl, .gipl.gz | yet | +| LSM | .lsm, .LSM | yet | +| MINC | .mnc, .MNC | yet | +| MRC | .mrc, .rec | yet | + +# Known limitations + +- Sections cannot be generated +- Time sequence volume not supported (will be supported soon) diff --git a/docs/misc.md b/docs/misc.md new file mode 100644 index 0000000..9fc53d0 --- /dev/null +++ b/docs/misc.md @@ -0,0 +1,20 @@ +# Future Features + +- Support more volumetric data formats (.nii, .map, .txm...) +- Generate sections +- More segmentation methods, e.g. AI segmentation. +- Even better shader for volumetric rendering + +### Bioxels + +Bioxels is based on the RAS coordinate system, Right Aanterior Superior, which was chosen over LPS because it is more compatible with most 3D CG software coordinate systems, and is in line with the 3D artist's understanding of space. + +All distances within Bioxels are in Units, and are specified in Meter pre unit. However, when Bioxels is imported into 3D CG software, its size in the software is not scaled by reading the Meter pre unit directly. The reason for this is that many 3D operations in software require that the primtives not be too large or too small. + +### Based on OpenVDB + +Bioxels is based entirely on OpenVDB for storage and rendering. The main reason for choosing OpenVDB is that as a volumetric data format, it is the fastest way to work with most CG renderers. + +### Based on Geometry Nodes + +Bioxel Nodes relies on Blender Geometry Nodes to reconstruct and render volumetric data. Node-based operations ensure that the original data is not permanently altered during reconstruction and rendering operations. The fact that the processing is based on Geometry Nodes without any additional dependencies also ensures that Blender can open files without this plugin installed. Look for more support for OpenVDB in GeometryNodes so that Bioxel Nodes can do more in the future. diff --git a/docs/nodes.md b/docs/nodes.md new file mode 100644 index 0000000..e69de29 diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css new file mode 100644 index 0000000..eb5b504 --- /dev/null +++ b/docs/stylesheets/extra.css @@ -0,0 +1,20 @@ +[data-md-color-scheme="slate"] { + --md-code-hl-string-color: #8b8b8b; + --md-code-hl-keyword-color: white; + --md-code-hl-number-color: white; + --md-typeset-a-color: white; +} + +[data-md-color-scheme="default"] { + --md-code-hl-string-color: #444444; + --md-code-hl-keyword-color: black; + --md-code-hl-number-color: black; +} + +[data-md-color-scheme=slate][data-md-color-primary=black] { + --md-typeset-a-color: white; +} + +[data-md-color-scheme=default][data-md-color-primary=black] { + --md-typeset-a-color: black; +} \ No newline at end of file diff --git a/mkdocs.yml b/mkdocs.yml new file mode 100644 index 0000000..ea795c7 --- /dev/null +++ b/mkdocs.yml @@ -0,0 +1,82 @@ +site_name: Bioxel Nodes Docs +site_url: https://omoolab.github.io/BioxelNodes/ +site_author: OmooLab +site_description: Bioxel Nodes is a Blender add-on for scientific volumetric data visualization. + +repo_name: OmooLab/BioxelNodes +repo_url: https://github.com/OmooLab/BioxelNodes + +nav: + - BioxelNodes: + - index.md + - Getting Started: getting-started.md + - Features: features.md + - Geometry Nodes: nodes.md + - Future Features: misc.md + +theme: + name: material + logo: assets/logo.png + language: en + font: + text: Open Sans + code: Cascadia Code + palette: + # Palette toggle for automatic mode + - media: "(prefers-color-scheme)" + primary: black + toggle: + icon: fontawesome/solid/circle-half-stroke + name: Switch to light mode + + # Palette toggle for light mode + - media: "(prefers-color-scheme: light)" + scheme: default + primary: black + toggle: + icon: fontawesome/regular/moon + name: Switch to dark mode + + # Palette toggle 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