diff --git a/README.md b/README.md index 72ab125..82be821 100644 --- a/README.md +++ b/README.md @@ -1,25 +1,26 @@ [δΈ­ζ–‡ζ–‡ζ‘£](https://uj6xfhbzp0.feishu.cn/wiki/Qx3VwHuNPimeI8kr6nDcvl1DnHf?from=from_copylink) -# πŸ¦– Bioxel Nodes +# 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 addon for scientific volumetric data visualization. It using Blender's powerful Geometry Nodes and Cycles to process and render volumetric data. You are free to share your blender file to anyone who does not install this extension, since most processes were done by Blender's native nodes. - -## About - -Before us, there have been many tutorials and addons for importing volumetric data into Blender. However, we found that there were many scientific issues that were not addressed in place, and the volume render results were not epic. With Bioxel Nodes, you can easily import any format volumetric data into Blender, and more importantly, make a beautiful realistic volume rendering quickly. - -Below are some examples with Bioxel Nodes. Thanks to Cycles Render, the volumetric data can be rendered with great detail: +Bioxel Nodes is a Blender addon for scientific volumetric data visualization. It using Blender's powerful **Geometry Nodes** and **Cycles** to process and render volumetric data. ![cover](https://omoolab.github.io/BioxelNodes/latest/assets/cover.png) -So how to use this extension? please check [Getting Started](https://omoolab.github.io/BioxelNodes/latest/getting-started) +- Fantastic rendering result, also support EEVEE NEXT +- Support multiple formats +- Support 4D volumetric data +- All kinds of cutters +- Simple and powerful nodes +- Based on blender natively, can work without addon. -## Supported Format +**Click [Getting Started](https://omoolab.github.io/BioxelNodes/latest/installation) to begin your journey into visualizing volumetric data!** + +## Support Multiple Formats | Format | EXT | Test | | ------ | ---------------------------------------- | ------- | @@ -30,40 +31,40 @@ So how to use this extension? please check [Getting Started](https://omoolab.git | TIFF | .tif, .TIF, .tiff, .TIFF | βœ… pass | | Nifti | .nia, .nii, .nii.gz, .hdr, .img, .img.gz | βœ… pass | | Nrrd | .nrrd, .nhdr | βœ… pass | -| Meta | .mha, .mhd | yet | | HDF5 | .hdf, .h4, .hdf4, .he2, .h5, .hdf5, .he5 | βœ… 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 +## Support 4D volumetric data + +![4d](https://omoolab.github.io/BioxelNodes/latest/assets/4d-time.gif) -- Cycles CPUs only, Cycles GPUs (Optix), EEVEE (partial support) -- Sections cannot be generated (will be supported soon) -- Time sequence volume not supported (will be supported soon) +πŸ₯° 4D volumetric data can also be imported into Blender. -## Compatibility to Newer Version +## Support EEVEE NEXT -Addon are updating, and it is possible that newer versions of the addon will not work on old project files properly. In order to make the old files work, you can do the following: +![eevee](https://omoolab.github.io/BioxelNodes/latest/assets/eevee.gif) -### For project files that need to be archived +πŸ‘ EEVEE NEXT is absolutely AWESOME! Bioxel Nodes is fully support EEVEE NEXT now! However, there are some limitations: -Persistently save the Addon nodes before the addon is updated. This will put the nodes out of sync with the addon functionality, but it will ensure that the entire file can be calculated and rendered correctly, it fit to project files that you need to archive. -Bioxel Nodes > Save All Staged Data +1. Only one cutter supported. +2. EEVEE result is not that great as Cycles does. -### For working project files +## Known Limitations -If you've ever done a persistent save of Bioxel Nodes nodes, it's possible that after the addon update, there may be new features of the addon that don't synergize with the saved nodes. In order for the new version to work with the old nodes, you need to relink them. -Bioxel Nodes > Relink Nodes to Addon +- Only works with Cycles CPU , Cycles GPU (OptiX), EEVEE +- Section surface cannot be generated when convert to mesh (will be supported soon) -## About EEVEE Render +## Compatibile to Newer Version -Bioxel Nodes is designed for Cycles Render. However, it does support eevee render partially.Also, there are some limitations: +**Updating this addon may break old files, so read the following carefully before updating** -1. Only one cutter supported. -2. EEVEE Render result is not that great as Cycles does. +Before updating this addon, you need to ask yourself whether this project file will be modified again or not, if it's an archived project file, I would recommend that you run **Bioxel Nodes > Save Staged Data** to make the addon nodes permanent. In this way, there will be no potential problem with the nodes not functioning due to the addon update. + +After the addon update, your old project files may not work either, this may be because you had executed **Save Staged Data**. If so, you need to execute **Bioxel Nodes > Relink Nodes to Addon** to relink them to make sure that the addon's new functionality and the addon nodes are synchronized. + +Also, unlike the newer versions, the older shaders are not based on OSL, so if you find that you can't render volumes, you need to turn on **Open Shading Language (OSL)** in the Render Settings. + +## Roadmap -> Volume Shader is not work properly in EEVEE Next since 4.2. It is because EEVEE Next is not support attributes from instances of volume shader by now. But Blender 4.3 is ok, so I suppose this issue will eventually be fixed. +- Better multi-format import experience +- One-click bake model with texture +- AI Segmentation to Generate Labels diff --git a/bioxelnodes/__init__.py b/bioxelnodes/__init__.py index c093c5c..754b6f0 100644 --- a/bioxelnodes/__init__.py +++ b/bioxelnodes/__init__.py @@ -9,7 +9,7 @@ "author": "Ma Nan", "description": "", "blender": (4, 1, 0), - "version": (0, 2, 6), + "version": (0, 2, 7), "location": "File -> Import", "warning": "", "category": "Node" diff --git a/bioxelnodes/assets/Nodes/BioxelNodes_4.1.blend b/bioxelnodes/assets/Nodes/BioxelNodes_4.1.blend index a4a66b7..df5fb34 100644 --- a/bioxelnodes/assets/Nodes/BioxelNodes_4.1.blend +++ b/bioxelnodes/assets/Nodes/BioxelNodes_4.1.blend @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:09e23fa95ee7262a284e2539ec5873e32100116ebaa17374c0bb97923c24aeb5 -size 6508765 +oid sha256:40dc55e26be78cb4b175df616bbba5d088c32ae027720fd2bb3f5f17dbdfef82 +size 6624975 diff --git a/bioxelnodes/io.py b/bioxelnodes/io.py index 7631683..f1de20d 100644 --- a/bioxelnodes/io.py +++ b/bioxelnodes/io.py @@ -13,7 +13,7 @@ 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_nodes_by_type, hide_in_ray, lock_transform, move_node_between_nodes, move_node_to_node, save_vdb, show_message) + get_nodes_by_type, hide_in_ray, lock_transform, move_node_between_nodes, move_node_to_node, save_vdb, save_vdbs, select_object, show_message) try: import SimpleITK as sitk @@ -124,7 +124,11 @@ def parse_volume_data(filepath: str, series_id=""): series_files = reader.GetGDCMSeriesFileNames( str(dir_path), series_id) reader.SetFileNames(series_files) + itk_volume = reader.Execute() + # for k in reader.GetMetaDataKeys(0): + # v = reader.GetMetaData(0, k) + # print(f'({k}) = = "{v}"') name = dir_path.name elif ext in SEQUENCE_EXTS: @@ -140,32 +144,64 @@ def parse_volume_data(filepath: str, series_id=""): itk_volume = sitk.ReadImage(filepath) name = Path(filepath).name.removesuffix(ext) - itk_volume = sitk.DICOMOrient(itk_volume, 'RAS') - volume = sitk.GetArrayFromImage(itk_volume) + # for key in itk_volume.GetMetaDataKeys(): + # print(f"{key},{itk_volume.GetMetaData(key)}") - if volume.ndim == 4: - volume = np.transpose(volume, (2, 1, 0, 3)) - else: - volume = np.transpose(volume) + if itk_volume.GetDimension() == 3: + itk_volume = sitk.DICOMOrient(itk_volume, 'RAS') + + meta = { + "name": name, + "shape": tuple(itk_volume.GetSize()), + "spacing": tuple(itk_volume.GetSpacing()), + "origin": tuple(itk_volume.GetOrigin()), + "direction": tuple(itk_volume.GetDirection()), + "is_oriented": True + } - meta = { - "name": name, - "shape": tuple(itk_volume.GetSize()), - "spacing": tuple(itk_volume.GetSpacing()), - "origin": tuple(itk_volume.GetOrigin()), - "direction": tuple(itk_volume.GetDirection()), - } + volume = sitk.GetArrayFromImage(itk_volume) - for key, value in meta.items(): - print(f"{key}: {value}") + # transpose ijk to kji + if volume.ndim == 4: + volume = np.transpose(volume, (2, 1, 0, 3)) + else: + volume = np.transpose(volume) + volume = np.expand_dims(volume, axis=-1) + + else: + # FIXME: not sure... + print(itk_volume.GetDirection()) + direction = np.array(itk_volume.GetDirection()) + direction = direction.reshape(3, 3) if itk_volume.GetDimension() == 3 \ + else direction.reshape(4, 4) + + direction = direction[1:, 1:] + direction = tuple(direction.flatten()) + + meta = { + "name": name, + "shape": tuple(itk_volume.GetSize()[:3]), + "spacing": tuple(itk_volume.GetSpacing()[:3]), + "origin": tuple(itk_volume.GetOrigin()[:3]), + "direction": direction, + "is_oriented": False + } + + volume = sitk.GetArrayFromImage(itk_volume) + + if volume.ndim == 5: + volume = np.transpose(volume, (0, 3, 2, 1, 4)) + else: + volume = np.transpose(volume, (0, 3, 2, 1)) + volume = np.expand_dims(volume, axis=-1) 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_label = "Volumetric Data as Bioxel Layer" + bl_description = "Import Volumetric Data as Bioxel Layer" bl_options = {'UNDO'} filepath: bpy.props.StringProperty( @@ -188,7 +224,7 @@ class ImportVolumeDataDialog(bpy.types.Operator): name="Read as", default="scalar", items=[("scalar", "Scalar", ""), - ("labels", "Labels", "")] + ("label", "Labels", "")] ) # type: ignore bioxel_size: bpy.props.FloatProperty( @@ -215,9 +251,14 @@ class ImportVolumeDataDialog(bpy.types.Operator): default=0.01, ) # type: ignore - do_orient: bpy.props.BoolProperty( - name="Orient to RAS", - default=True, + is_time_sequence: bpy.props.BoolProperty( + name="Is Time Sequence", + default=False, + ) # type: ignore + + split_channels: bpy.props.BoolProperty( + name="Split Channels", + default=False, ) # type: ignore def execute(self, context): @@ -259,10 +300,8 @@ def execute(self, context): 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 + transfrom = mat_lps2ras @ mat_location @ mat_rotation @ mat_scale \ + if meta['is_oriented'] else mat_location @ mat_rotation @ mat_scale # Wrapper a Container if not self.container: @@ -308,26 +347,62 @@ def execute(self, context): container_node_group = container.modifiers[0].node_group preferences = context.preferences.addons[__package__].preferences - loc, rot, sca = transfrom.decompose() + # TODO: change to transform when 4.2? + 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 + def create_layer(volume, layer_name, layer_shape, layer_type="scalar"): + if volume.ndim == 4: + grids_sequence = [] + for f in range(volume.shape[0]): + print(f"Resampling...") + frame = ski.resize(volume[f, :, :, :], + layer_shape, + preserve_range=True, + anti_aliasing=volume.dtype.kind != "b") + + grid = vdb.FloatGrid() + frame = frame.copy().astype(np.float32) + grid.copyFromArray(frame) + grid.transform = vdb.createLinearTransform( + transfrom.transposed()) + grid.name = layer_type + grids_sequence.append([grid]) + + vdb_paths = save_vdbs(grids_sequence, context) + + # Read VDB + print(f"Loading the cache to Blender scene...") + files = [{"name": str(vdb_path.name), "name": str(vdb_path.name)} + for vdb_path in vdb_paths] + + bpy.ops.object.volume_import(filepath=str(vdb_paths[0]), directory=str(vdb_paths[0].parent), + files=files, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1)) + + else: + volume = ski.resize(volume, + layer_shape, + preserve_range=True, + anti_aliasing=volume.dtype.kind != "b") + + 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) + 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)) + # 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 + layer.data.sequence_mode = 'REPEAT' # Set props to VDB object layer.name = layer_name @@ -368,7 +443,7 @@ def create_layer(volume, layer_name, layer_type="scalar"): output_node.inputs[0]) # for compatibility to old vdb - to_layer_node.inputs['Not Transfromed'].default_value = True + # to_layer_node.inputs['Not Transfromed'].default_value = True to_layer_node.inputs['Layer ID'].default_value = random.randint(-200000000, 200000000) to_layer_node.inputs['Data Type'].default_value = dtype_index @@ -381,96 +456,118 @@ def create_layer(volume, layer_name, layer_type="scalar"): return layer - if self.read_as == "labels": + def create_mask_node(layer, node_type, node_label, offset): + mask_node = custom_nodes.add_node(container_node_group, + node_type) + mask_node.label = node_label + mask_node.inputs[0].default_value = layer + + # Connect to output if no output linked + output_node = get_nodes_by_type(container_node_group, + 'NodeGroupOutput')[0] + if len(output_node.inputs[0].links) == 0: + container_node_group.links.new(mask_node.outputs[0], + output_node.inputs[0]) + move_node_to_node(mask_node, output_node, (-300, 0)) + else: + move_node_to_node(mask_node, output_node, offset) + + # change shape as sequence or not + if self.is_time_sequence: + # 4->5 or 5->5 if volume.ndim == 4: - volume = np.amax(volume, -1) + # channel as frame + volume = volume.transpose(3, 0, 1, 2) + volume = np.expand_dims(volume, axis=-1) + + else: + # 4->4 or 5->4 + if volume.ndim == 5: + # select frame 0 + volume = volume[0, :, :, :, :] + + if self.read_as == "label": + layer_name = self.layer_name or "Label" + 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, - layer_shape, - preserve_range=True, - anti_aliasing=False) + layer_name_i = f"{layer_name}_{i+1}" + layer = create_layer(volume=label, - layer_name=f"{container_name}_{layer_name}_{i+1}", + layer_name=f"{container_name}_{layer_name_i}", + layer_shape=layer_shape, layer_type="label") - mask_node = custom_nodes.add_node(container_node_group, - '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_nodes_by_type(container_node_group, - 'NodeGroupOutput')[0] - if len(output_node.inputs[0].links) == 0: - container_node_group.links.new(mask_node.outputs[0], - output_node.inputs[0]) - move_node_to_node(mask_node, output_node, (-300, 0)) - else: - move_node_to_node(mask_node, output_node, - (0, -100 * (i+1))) + mask_node = create_mask_node(layer=layer, + node_type='BioxelNodes_MaskByLabel', + node_label=layer_name_i, + offset=(0, -100 * (i+1))) 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! + layer_name = self.layer_name or "Scalar" + # 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)) + if self.split_channels: + for i in range(volume.shape[-1]): + scalar = volume[:, :, :, :, + 0] if self.is_time_sequence else volume[:, :, :, i] + orig_max = float(np.max(scalar)) + orig_min = float(np.min(scalar)) + + scalar_offset = 0 + if orig_min < 0: + scalar_offset = -orig_min + scalar = scalar + np.full_like(scalar, scalar_offset) + + layer_name_i = f"{layer_name}_{i+1}" + layer = create_layer(volume=scalar, + layer_name=f"{container_name}_{layer_name_i}", + layer_shape=layer_shape, + layer_type="scalar") + + layer_node_group = layer.modifiers[0].node_group + to_layer_node = layer_node_group.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 + + mask_node = create_mask_node(layer=layer, + node_type='BioxelNodes_MaskByThreshold', + node_label=layer_name_i, + offset=(0, -100 * (i+1))) - 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") + else: + volume = np.amax(volume, -1) + orig_max = float(np.max(volume)) + orig_min = float(np.min(volume)) - layer_node_group = layer.modifiers[0].node_group - to_layer_node = layer_node_group.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 + scalar_offset = 0 + if orig_min < 0: + scalar_offset = -orig_min + volume = volume + np.full_like(volume, scalar_offset) - mask_node = custom_nodes.add_node(container_node_group, - 'BioxelNodes_MaskByThreshold') - mask_node.label = layer_name - mask_node.inputs[0].default_value = layer + layer = create_layer(volume=volume, + layer_name=f"{container_name}_{layer_name}", + layer_shape=layer_shape, + layer_type="scalar") - # Connect to output if no output linked - output_node = get_nodes_by_type(container_node_group, - 'NodeGroupOutput')[0] + layer_node_group = layer.modifiers[0].node_group + to_layer_node = layer_node_group.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 - if len(output_node.inputs[0].links) == 0: - container_node_group.links.new(mask_node.outputs[0], - output_node.inputs[0]) - move_node_to_node(mask_node, output_node, (-300, 0)) - else: - move_node_to_node(mask_node, output_node, (0, -100)) + mask_node = create_mask_node(layer=layer, + node_type='BioxelNodes_MaskByThreshold', + node_label=layer_name, + offset=(0, -100)) - bpy.context.view_layer.objects.active = container + select_object(container) # Change render setting for better result if preferences.do_change_render_setting and is_first_import: @@ -492,7 +589,7 @@ def create_layer(volume, layer_name, layer_type="scalar"): return {'FINISHED'} def invoke(self, context, event): - if self.read_as == "labels": + if self.read_as == "label": volume_dtype = "Label" elif self.read_as == "scalar": volume_dtype = "Scalar" @@ -529,6 +626,11 @@ def draw(self, context): row.prop(self, "orig_spacing") panel.label(text=layer_shape_text) + panel = layout.box() + panel.prop(self, "is_time_sequence") + if self.read_as == "scalar": + panel.prop(self, "split_channels") + if self.container == "": panel = layout.box() panel.prop(self, "scene_scale") @@ -550,8 +652,8 @@ def get_series_ids(self, context): 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_label = "Volumetric Data as Bioxel Layer" + bl_description = "Import Volumetric Data as Bioxel Layer" bl_options = {'UNDO'} filepath: bpy.props.StringProperty(subtype="FILE_PATH") # type: ignore @@ -562,7 +664,7 @@ class ParseVolumeData(bpy.types.Operator): name="Read as", default="scalar", items=[("scalar", "Scalar", ""), - ("labels", "Labels", "")] + ("label", "Labels", "")] ) # type: ignore series_id: bpy.props.EnumProperty( @@ -581,13 +683,17 @@ def execute(self, context): print("Collecting Meta Data...") volume, meta = parse_volume_data(self.filepath) - if self.read_as == "labels": + + for key, value in meta.items(): + print(f"{key}: {value}") + + if self.read_as == "label": not_int = volume.dtype.kind != "b" and volume.dtype.kind != "i" and volume.dtype.kind != "u" too_large = np.max(volume) > 100 if not_int or too_large: self.report( - {"WARNING"}, "This volume data does not looks like labels, please check again.") + {"WARNING"}, "This volume data does not looks like label, please check again.") return {'CANCELLED'} # do_orient = ext not in SEQUENCE_EXTS or ext in DICOM_EXTS @@ -704,15 +810,15 @@ def invoke(self, context, event): 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" + bl_description = "Import Volumetric 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" + bl_label = "Import as Label" + bl_description = "Import Volumetric Data to Container as Label" + read_as = "label" try: @@ -729,40 +835,10 @@ def poll_drop(cls, context): ... -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 Bioxel as VDB" - bl_description = "Export Bioxel Layer as VDB" + bl_label = "Export Layer as VDB" + bl_description = "Export Layer as VDB" bl_options = {'UNDO'} filepath: bpy.props.StringProperty( diff --git a/bioxelnodes/menus.py b/bioxelnodes/menus.py index e15eedf..fd19074 100644 --- a/bioxelnodes/menus.py +++ b/bioxelnodes/menus.py @@ -1,12 +1,24 @@ import bpy -from .operators import (AddPlaneCutter, AddCylinderCutter, AddCubeCutter, AddSphereCutter, CombineLabels, - ConvertToMesh, InvertScalar, FillByLabel, FillByThreshold, FillByRange) -from .io import ExportVolumeData, ImportAsLabelLayer, ImportAsScalarLayer, ImportVolumeData, AddVolumeData -from .save import ReLinkNodes, SaveLayers, SaveAllToShare +from .utils import get_container_from_selection +from .operators import (AddPieCutter, AddPlaneCutter, AddCylinderCutter, AddCubeCutter, AddSphereCutter, CombineLabels, + ConvertToMesh, InvertScalar, FillByLabel, FillByThreshold, FillByRange, PickBboxWire, PickMesh, PickVolume) +from .io import ExportVolumeData, ImportAsLabelLayer, ImportAsScalarLayer +from .save import CleanAllCaches, ReLinkNodes, SaveLayers, SaveStagedData -class ModifyLayer(bpy.types.Menu): +class PickFromContainerMenu(bpy.types.Menu): + bl_idname = "BIOXELNODES_MT_PICK" + bl_label = "Pick from Container" + + def draw(self, context): + layout = self.layout + layout.operator(PickMesh.bl_idname) + layout.operator(PickVolume.bl_idname) + layout.operator(PickBboxWire.bl_idname) + + +class ModifyLayerMenu(bpy.types.Menu): bl_idname = "BIOXELNODES_MT_MODIFY_LAYERS" bl_label = "Modify Layer" @@ -25,20 +37,21 @@ class AddCutterMenu(bpy.types.Menu): def draw(self, context): layout = self.layout - layout.operator(AddPlaneCutter.bl_idname) - layout.operator(AddCylinderCutter.bl_idname) - layout.operator(AddCubeCutter.bl_idname) - layout.operator(AddSphereCutter.bl_idname) + layout.operator(AddPlaneCutter.bl_idname, text="Plane Cutter") + layout.operator(AddCylinderCutter.bl_idname, text="Cylinder Cutter") + layout.operator(AddCubeCutter.bl_idname, text="Cube Cutter") + layout.operator(AddSphereCutter.bl_idname, text="Sphere Cutter") + layout.operator(AddPieCutter.bl_idname, text="Pie Cutter") class ImportLayerMenu(bpy.types.Menu): bl_idname = "BIOXELNODES_MT_LAYERS" - bl_label = "Import Volume Data as Bioxel" + bl_label = "Import Volumetric Data" def draw(self, context): layout = self.layout - layout.operator(ImportAsScalarLayer.bl_idname) - layout.operator(ImportAsLabelLayer.bl_idname) + layout.operator(ImportAsScalarLayer.bl_idname, text="as Scalar") + layout.operator(ImportAsLabelLayer.bl_idname, text="as Label") class BioxelNodesView3DMenu(bpy.types.Menu): @@ -47,9 +60,24 @@ class BioxelNodesView3DMenu(bpy.types.Menu): def draw(self, context): layout = self.layout - layout.menu(ImportLayerMenu.bl_idname) - layout.menu(AddCutterMenu.bl_idname) - layout.operator(ConvertToMesh.bl_idname) + containers = get_container_from_selection() + is_selected = len(containers) > 0 + layout.operator(ImportAsScalarLayer.bl_idname, + text=ImportAsScalarLayer.bl_label+" (Add to)" + if is_selected else ImportAsScalarLayer.bl_label+" (Init)") + layout.operator(ImportAsLabelLayer.bl_idname, + text=ImportAsLabelLayer.bl_label+" (Add to)" + if is_selected else ImportAsLabelLayer.bl_label+" (Init)") + layout.separator() + layout.operator(AddPlaneCutter.bl_idname) + layout.operator(AddCylinderCutter.bl_idname) + layout.operator(AddCubeCutter.bl_idname) + layout.operator(AddSphereCutter.bl_idname) + layout.operator(AddPieCutter.bl_idname) + layout.separator() + layout.operator(PickMesh.bl_idname) + layout.operator(PickVolume.bl_idname) + layout.operator(PickBboxWire.bl_idname) layout.separator() layout.operator(SaveLayers.bl_idname) @@ -60,25 +88,51 @@ class BioxelNodesOutlinerMenu(bpy.types.Menu): def draw(self, context): layout = self.layout - layout.menu(ImportLayerMenu.bl_idname) - layout.menu(AddCutterMenu.bl_idname) - layout.operator(ConvertToMesh.bl_idname) + containers = get_container_from_selection() + is_selected = len(containers) > 0 + layout.operator(ImportAsScalarLayer.bl_idname, + text=ImportAsScalarLayer.bl_label+" (Add to)" + if is_selected else ImportAsScalarLayer.bl_label+" (Init)") + layout.operator(ImportAsLabelLayer.bl_idname, + text=ImportAsLabelLayer.bl_label+" (Add to)" + if is_selected else ImportAsLabelLayer.bl_label+" (Init)") layout.separator() - layout.menu(ModifyLayer.bl_idname) + layout.operator(AddPlaneCutter.bl_idname) + layout.operator(AddCylinderCutter.bl_idname) + layout.operator(AddCubeCutter.bl_idname) + layout.operator(AddSphereCutter.bl_idname) + layout.operator(AddPieCutter.bl_idname) + layout.separator() + layout.operator(PickMesh.bl_idname) + layout.operator(PickVolume.bl_idname) + layout.operator(PickBboxWire.bl_idname) layout.separator() layout.operator(SaveLayers.bl_idname) + layout.separator() + layout.operator(InvertScalar.bl_idname) + layout.operator(FillByThreshold.bl_idname) + layout.operator(FillByRange.bl_idname) + layout.operator(FillByLabel.bl_idname) + layout.operator(CombineLabels.bl_idname) + layout.separator() + layout.operator(ExportVolumeData.bl_idname) def TOPBAR_FILE_IMPORT(self, context): layout = self.layout + containers = get_container_from_selection() + is_selected = len(containers) > 0 + layout.separator() - layout.menu(ImportLayerMenu.bl_idname) + layout.menu(ImportLayerMenu.bl_idname, text="Volumetric Data as Bioxel (Add to)" + if is_selected else "Volumetric Data as Bioxel (Init)") def TOPBAR_FILE_EXPORT(self, context): layout = self.layout layout.separator() - layout.operator(ExportVolumeData.bl_idname) + layout.operator(ExportVolumeData.bl_idname, + text="Bioxel Layer (.vdb)") def VIEW3D_OBJECT(self, context): @@ -99,14 +153,19 @@ class BioxelNodesTopbarMenu(bpy.types.Menu): def draw(self, context): layout = self.layout - layout.menu(ImportLayerMenu.bl_idname) - layout.operator(ExportVolumeData.bl_idname) + containers = get_container_from_selection() + is_selected = len(containers) > 0 + + layout.menu(ImportLayerMenu.bl_idname, text=ImportLayerMenu.bl_label+" (Add to)" + if is_selected else ImportLayerMenu.bl_label+" (Init)") layout.separator() layout.menu(AddCutterMenu.bl_idname) - layout.operator(ConvertToMesh.bl_idname) + layout.menu(PickFromContainerMenu.bl_idname) layout.separator() - layout.operator(SaveAllToShare.bl_idname) + layout.operator(SaveStagedData.bl_idname) layout.operator(ReLinkNodes.bl_idname) + layout.separator() + layout.operator(CleanAllCaches.bl_idname) def TOPBAR(self, context): diff --git a/bioxelnodes/nodes.py b/bioxelnodes/nodes.py index 9b2a6a4..55a6bcc 100644 --- a/bioxelnodes/nodes.py +++ b/bioxelnodes/nodes.py @@ -203,6 +203,12 @@ 'icon': 'MESH_UVSPHERE', 'node_type': 'BioxelNodes_SphereObjectCutter', 'node_description': '', + }, + { + 'label': 'Pie Cutter', + 'icon': 'MESH_CONE', + 'node_type': 'BioxelNodes_PieObjectCutter', + 'node_description': '', } ] }, diff --git a/bioxelnodes/operators.py b/bioxelnodes/operators.py index 21ab4b6..5760139 100644 --- a/bioxelnodes/operators.py +++ b/bioxelnodes/operators.py @@ -3,12 +3,12 @@ import bpy import pyopenvdb as vdb import numpy as np - +import bmesh from . import skimage as ski from . import scipy from .nodes import custom_nodes from .utils import (get_container, get_container_from_selection, get_container_layers, - get_layer, get_nodes_by_type, hide_in_ray, lock_transform, move_node_between_nodes, move_node_to_node, save_vdb) + get_layer, get_nodes_by_type, hide_in_ray, lock_transform, move_node_between_nodes, move_node_to_node, save_vdb, select_object) def get_layer_name(layer): @@ -105,6 +105,7 @@ def deep_copy_layer(vdb_path, base_layer, name): # add convert to layer node base_layer_node = base_layer.modifiers[0].node_group.nodes['BioxelNodes__ConvertToLayer'] + not_transformed = base_layer_node.inputs['Not Transfromed'].default_value dtype_index = base_layer_node.inputs['Data Type'].default_value bioxel_size = base_layer_node.inputs['Bioxel Size'].default_value layer_shape = base_layer_node.inputs['Shape'].default_value @@ -127,7 +128,7 @@ def deep_copy_layer(vdb_path, base_layer, name): node_group.links.new(copyed_layer_node.outputs[0], output_node.inputs[0]) # for compatibility to old vdb - copyed_layer_node.inputs['Not Transfromed'].default_value = True + copyed_layer_node.inputs['Not Transfromed'].default_value = not_transformed copyed_layer_node.inputs['Layer ID'].default_value = random.randint(-200000000, 200000000) copyed_layer_node.inputs['Data Type'].default_value = dtype_index @@ -291,14 +292,14 @@ def execute(self, context): "BioxelNodes_MaskByThreshold", inverted_layer_name) - bpy.context.view_layer.objects.active = container + select_object(container) return {'FINISHED'} class FillByThreshold(bpy.types.Operator): bl_idname = "bioxelnodes.fill_by_threshold" - bl_label = "Fill by Threshold" + bl_label = "Fill Value by Threshold" bl_description = "Fill Value by Threshold" bl_options = {'UNDO'} @@ -358,7 +359,7 @@ def execute(self, context): mask_node.inputs[1].default_value = self.threshold - bpy.context.view_layer.objects.active = container + select_object(container) return {'FINISHED'} @@ -372,7 +373,7 @@ def invoke(self, context, event): class FillByRange(bpy.types.Operator): bl_idname = "bioxelnodes.fill_by_range" - bl_label = "Fill by Range" + bl_label = "Fill Value by Range" bl_description = "Fill Value by Range" bl_options = {'UNDO'} @@ -441,7 +442,7 @@ def execute(self, context): mask_node.inputs[1].default_value = self.from_min - bpy.context.view_layer.objects.active = container + select_object(container) return {'FINISHED'} @@ -455,7 +456,7 @@ def invoke(self, context, event): class FillByLabel(bpy.types.Operator): bl_idname = "bioxelnodes.fill_by_label" - bl_label = "Fill by Label" + bl_label = "Fill Value by Label" bl_description = "Fill Value by Label Area" bl_options = {'UNDO'} @@ -525,7 +526,7 @@ def execute(self, context): "BioxelNodes_MaskByThreshold", filled_layer_name) - bpy.context.view_layer.objects.active = container + select_object(container) return {'FINISHED'} @@ -585,14 +586,14 @@ def execute(self, context): "BioxelNodes_MaskByLabel", combined_layer_name) - bpy.context.view_layer.objects.active = container + select_object(container) return {'FINISHED'} class ConvertToMesh(bpy.types.Operator): bl_idname = "bioxelnodes.convert_to_mesh" - bl_label = "Convert Container To Mesh" - bl_description = "Convert Bioxel Container To Mesh" + bl_label = "Convert To Mesh" + bl_description = "Convert Container To Mesh" bl_options = {'UNDO'} @classmethod @@ -633,16 +634,147 @@ def execute(self, context): # constraint=mesh.constraints[0].name, owner='OBJECT') bpy.ops.object.modifier_apply(modifier=mesh.modifiers[0].name) - bpy.context.object.active_material_index = 1 - bpy.ops.object.material_slot_remove() - - bpy.context.view_layer.objects.active = mesh + select_object(mesh) self.report({"INFO"}, f"Successfully convert to mesh") return {'FINISHED'} +class PickMesh(bpy.types.Operator): + bl_idname = "bioxelnodes.pick_mesh" + bl_label = "Pick Mesh" + bl_description = "Pick Container Mesh" + bl_options = {'UNDO'} + + @classmethod + def poll(cls, context): + containers = get_container_from_selection() + return len(containers) > 0 + + def execute(self, context): + containers = get_container_from_selection() + + if len(containers) == 0: + self.report({"WARNING"}, "Cannot find any bioxel container.") + return {'FINISHED'} + + container = containers[0] + + bpy.ops.mesh.primitive_cube_add( + size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1)) + mesh = bpy.context.active_object + + mesh.name = f"Mesh_{container.name}" + + bpy.ops.node.new_geometry_nodes_modifier() + modifier = mesh.modifiers[0] + node_group = modifier.node_group + + output_node = get_nodes_by_type(node_group, 'NodeGroupOutput')[0] + pick_mesh_node = custom_nodes.add_node(node_group, + "BioxelNodes_PickMesh") + + pick_mesh_node.inputs[0].default_value = container + node_group.links.new(pick_mesh_node.outputs[0], output_node.inputs[0]) + + select_object(mesh) + + self.report({"INFO"}, f"Successfully picked mesh") + + return {'FINISHED'} + + +class PickVolume(bpy.types.Operator): + bl_idname = "bioxelnodes.pick_volume" + bl_label = "Pick Volume" + bl_description = "Pick Container Volume" + bl_options = {'UNDO'} + + @classmethod + def poll(cls, context): + containers = get_container_from_selection() + return len(containers) > 0 + + def execute(self, context): + containers = get_container_from_selection() + + if len(containers) == 0: + self.report({"WARNING"}, "Cannot find any bioxel container.") + return {'FINISHED'} + + container = containers[0] + + bpy.ops.mesh.primitive_cube_add( + size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1)) + volume = bpy.context.active_object + + volume.name = f"Volume_{container.name}" + + bpy.ops.node.new_geometry_nodes_modifier() + modifier = volume.modifiers[0] + node_group = modifier.node_group + + output_node = get_nodes_by_type(node_group, 'NodeGroupOutput')[0] + pick_volume_node = custom_nodes.add_node(node_group, + "BioxelNodes_PickVolume") + + pick_volume_node.inputs[0].default_value = container + node_group.links.new( + pick_volume_node.outputs[0], output_node.inputs[0]) + + select_object(volume) + + self.report({"INFO"}, f"Successfully picked volume") + + return {'FINISHED'} + + +class PickBboxWire(bpy.types.Operator): + bl_idname = "bioxelnodes.pick_bbox_wire" + bl_label = "Pick Bbox Wire" + bl_description = "Pick Container Bbox Wire" + bl_options = {'UNDO'} + + @classmethod + def poll(cls, context): + containers = get_container_from_selection() + return len(containers) > 0 + + def execute(self, context): + containers = get_container_from_selection() + + if len(containers) == 0: + self.report({"WARNING"}, "Cannot find any bioxel container.") + return {'FINISHED'} + + container = containers[0] + + bpy.ops.mesh.primitive_cube_add( + size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1)) + bbox_wire = bpy.context.active_object + + bbox_wire.name = f"Wire_{container.name}" + + bpy.ops.node.new_geometry_nodes_modifier() + modifier = bbox_wire.modifiers[0] + node_group = modifier.node_group + + output_node = get_nodes_by_type(node_group, 'NodeGroupOutput')[0] + pick_bbox_wire_node = custom_nodes.add_node(node_group, + "BioxelNodes_PickBboxWire") + + pick_bbox_wire_node.inputs[0].default_value = container + node_group.links.new( + pick_bbox_wire_node.outputs[0], output_node.inputs[0]) + + select_object(bbox_wire) + + self.report({"INFO"}, f"Successfully picked bbox wire") + + return {'FINISHED'} + + class AddCutter(): bl_options = {'UNDO'} @@ -677,6 +809,40 @@ def execute(self, context): node_type = "BioxelNodes_SphereObjectCutter" bpy.ops.mesh.primitive_ico_sphere_add( radius=1, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1)) + elif self.object_type == "pie": + node_type = "BioxelNodes_PieObjectCutter" + # Create mesh + pie_mesh = bpy.data.meshes.new('Pie') + + # Create object + pie = bpy.data.objects.new('Pie', pie_mesh) + + # Link object to scene + bpy.context.scene.collection.objects.link(pie) + # Get a BMesh representation + bm = bmesh.new() # create an empty BMesh + bm.from_mesh(pie_mesh) # fill it in from a Mesh + + # Hot to create vertices + v_0 = bm.verts.new((0.0, -1.0, 0.0)) + v_1 = bm.verts.new((-1.0, -1.0, 1.0)) + v_2 = bm.verts.new((0.0, 1.0, 0.0)) + v_3 = bm.verts.new((-1.0, 1.0, 1.0)) + v_4 = bm.verts.new((1.0, -1.0, 1.0)) + v_5 = bm.verts.new((1.0, 1.0, 1.0)) + + # Initialize the index values of this sequence. + bm.verts.index_update() + + # How to create a face + # it's not necessary to create the edges before, I made it only to show how create + # edges too + bm.faces.new((v_0, v_1, v_3, v_2)) + bm.faces.new((v_0, v_2, v_5, v_4)) + + # Finish up, write the bmesh back to the mesh + bm.to_mesh(pie_mesh) + bpy.context.view_layer.objects.active = pie cutter = bpy.context.active_object cutter.visible_camera = False @@ -692,7 +858,7 @@ def execute(self, context): node_group = modifier.node_group cutter_node = custom_nodes.add_node(node_group, node_type) cutter_node.inputs[0].default_value = cutter - + cut_nodes = get_nodes_by_type(node_group, 'BioxelNodes_Cut') output_node = get_nodes_by_type(node_group, 'NodeGroupOutput')[0] @@ -715,9 +881,10 @@ def execute(self, context): cut_node.inputs[1]) move_node_to_node(cutter_node, cut_node, (-300, -300)) + select_object(cutter) else: move_node_to_node(cutter_node, output_node, (0, -100)) - bpy.context.view_layer.objects.active = container + select_object(container) return {'FINISHED'} @@ -752,3 +919,11 @@ class AddSphereCutter(bpy.types.Operator, AddCutter): bl_description = "Add a Sphere Cutter to Container" bl_options = {'UNDO'} object_type = "sphere" + + +class AddPieCutter(bpy.types.Operator, AddCutter): + bl_idname = "bioxelnodes.add_pie_cutter" + bl_label = "Add a Pie Cutter" + bl_description = "Add a Pie Cutter to Container" + bl_options = {'UNDO'} + object_type = "pie" diff --git a/bioxelnodes/save.py b/bioxelnodes/save.py index bedd613..eb2869a 100644 --- a/bioxelnodes/save.py +++ b/bioxelnodes/save.py @@ -1,7 +1,8 @@ +import re import bpy from pathlib import Path import shutil -from .utils import get_all_layers, get_container, get_container_layers +from .utils import copy_to_dir, get_all_layers, get_container, get_container_from_selection, get_container_layers from .nodes import custom_nodes CLASS_PREFIX = "BIOXELNODES_MT_NODES" @@ -26,18 +27,18 @@ def execute(self, context): return {'FINISHED'} -class SaveAllToShare(bpy.types.Operator): - bl_idname = "bioxelnodes.save_all_to_share" - bl_label = "Save All Staged Data" - bl_description = "Save all staged data for sharing" +class SaveStagedData(bpy.types.Operator): + bl_idname = "bioxelnodes.save_staged_data" + bl_label = "Save Staged Data" + bl_description = "Save all staged data in this file for sharing" save_layer: bpy.props.BoolProperty( name="Save Layer VDB Cache", default=True, ) # type: ignore - layer_dir: bpy.props.StringProperty( - name="Layer Directory", + cache_dir: bpy.props.StringProperty( + name="Cache Directory", subtype='DIR_PATH', default="//" ) # type: ignore @@ -83,15 +84,18 @@ def execute(self, context): self.report({"INFO"}, f"Successfully saved to {output_path}") if self.save_layer: - layers = get_all_layers() - for layer in layers: + fails = [] + for layer in get_all_layers(): try: - save_layer(layer, self.layer_dir) + save_layer(layer, self.cache_dir) except: - self.report( - {"WARNING"}, f"Fail to save {layer.name}, skiped") + fails.append(layer) - self.report({"INFO"}, f"Successfully saved bioxel layers.") + if len(fails) == 0: + self.report({"INFO"}, f"Successfully saved bioxel layers.") + else: + self.report( + {"WARNING"}, f"{','.join([layer.name for layer in fails])} fail to save.") return {'FINISHED'} @@ -108,36 +112,43 @@ def draw(self, context): layout = self.layout panel = layout.box() panel.prop(self, "save_layer") - panel.prop(self, "layer_dir") + panel.prop(self, "cache_dir") panel = layout.box() panel.prop(self, "save_lib") panel.prop(self, "lib_dir") def save_layer(layer, output_dir): - name = layer.name + + pattern = r'\.\d{4}\.' # "//" output_dir = bpy.path.abspath(output_dir) source_dir = bpy.path.abspath(layer.data.filepath) - output_path: Path = Path(output_dir, f"{name}.vdb").resolve() source_path: Path = Path(source_dir).resolve() + is_sequence = re.search(pattern, source_path.name) is not None + name = layer.name if is_sequence else f"{layer.name}.vdb" + output_path: Path = Path(output_dir, name, source_path.name).resolve() \ + if is_sequence else Path(output_dir, name).resolve() if output_path != source_path: - shutil.copy(source_path, output_path) + copy_to_dir(source_path.parent if is_sequence else source_path, + output_path.parent.parent if is_sequence else output_path.parent, + new_name=name) blend_path = Path(bpy.path.abspath("//")).resolve() + layer.data.filepath = bpy.path.relpath( str(output_path), start=str(blend_path)) class SaveLayers(bpy.types.Operator): bl_idname = "bioxelnodes.save_layers" - bl_label = "Save Container's Layers" - bl_description = "Save Bioxel Layers to Directory." + bl_label = "Save Layers" + bl_description = "Save Container Layers to Directory." - layer_dir: bpy.props.StringProperty( + cache_dir: bpy.props.StringProperty( name="Layer Directory", subtype='DIR_PATH', default="//" @@ -145,24 +156,29 @@ class SaveLayers(bpy.types.Operator): @classmethod def poll(cls, context): - container = get_container(bpy.context.active_object) - return True if container else False + containers = get_container_from_selection() + return len(containers) > 0 def execute(self, context): - container = get_container(bpy.context.active_object) + containers = get_container_from_selection() - if not container: + if len(containers) == 0: self.report({"WARNING"}, "Cannot find any bioxel container.") return {'FINISHED'} - for layer in get_container_layers(container): - try: - save_layer(layer, self.layer_dir) - except: - self.report( - {"WARNING"}, f"Fail to save {layer.name}, skiped") + fails = [] + for container in containers: + for layer in get_container_layers(container): + try: + save_layer(layer, self.cache_dir) + except: + fails.append(layer) - self.report({"INFO"}, f"Successfully saved bioxel layers.") + if len(fails) == 0: + self.report({"INFO"}, f"Successfully saved bioxel layers.") + else: + self.report( + {"WARNING"}, f"{','.join([layer.name for layer in fails])} fail to save.") return {'FINISHED'} @@ -170,3 +186,27 @@ def invoke(self, context, event): context.window_manager.invoke_props_dialog(self, width=500) return {'RUNNING_MODAL'} + + +class CleanAllCaches(bpy.types.Operator): + bl_idname = "bioxelnodes.clear_all_caches" + bl_label = "Clean All Caches in Temp" + bl_description = "Clean all caches saved in temp" + + def execute(self, context): + preferences = context.preferences.addons[__package__].preferences + cache_dir = Path(preferences.cache_dir, 'VDBs') + try: + shutil.rmtree(cache_dir) + self.report({"INFO"}, f"Successfully cleaned caches.") + return {'FINISHED'} + except: + self.report({"WARNING"}, + "Fail to clean caches, you may do it manually.") + return {'CANCELLED'} + + def invoke(self, context, event): + context.window_manager.invoke_confirm(self, + event, + message="All caches will be cleaned, include other project files, do you still want to clean?") + return {'RUNNING_MODAL'} diff --git a/bioxelnodes/utils.py b/bioxelnodes/utils.py index c3a8b1e..9879697 100644 --- a/bioxelnodes/utils.py +++ b/bioxelnodes/utils.py @@ -3,6 +3,45 @@ from pathlib import Path import pyopenvdb as vdb from uuid import uuid4 +import shutil + + +def select_object(target_obj): + for obj in bpy.data.objects: + obj.select_set(False) + + target_obj.select_set(True) + bpy.context.view_layer.objects.active = target_obj + + +def copy_to_dir(source_path, dir_path, new_name=None, exist_ok=True): + source = Path(source_path) + target = Path(dir_path) + + # Check if the source exists + if not source.exists(): + raise FileNotFoundError + + # Check if the target exists + if not target.exists(): + target.mkdir(parents=True, exist_ok=True) + + target_path = target / new_name if new_name else target / source.name + # If source is a file, copy it to the target directory + if source.is_file(): + try: + shutil.copy(source, target_path) + except shutil.SameFileError: + if exist_ok: + pass + else: + raise shutil.SameFileError + # If source is a directory, copy its contents to the target directory + elif source.is_dir(): + shutil.copytree(source, target_path, dirs_exist_ok=exist_ok) + + if not target_path.exists(): + raise Exception def move_node_to_node(node, target_node, offset=(0, 0)): @@ -124,13 +163,35 @@ def save_vdb(grids, context): return vdb_path +def save_vdbs(grids_sequence, context): + preferences = context.preferences.addons[__package__].preferences + cache_dir = Path(preferences.cache_dir, 'VDBs') + cache_dir.mkdir(parents=True, exist_ok=True) + vdb_name = str(uuid4()) + vdb_dir_path = Path(cache_dir, vdb_name) + vdb_dir_path.mkdir(parents=True, exist_ok=True) + + vdb_paths = [] + for f, grids in enumerate(grids_sequence): + vdb_path = Path(vdb_dir_path, f"{vdb_name}.{str(f+1).zfill(4)}.vdb") + print(f"Storing the VDB file ({str(vdb_path)})...") + vdb.write(str(vdb_path), grids=grids) + vdb_paths.append(vdb_path) + + return vdb_paths + + def get_container_from_selection(): containers = [] for obj in bpy.context.selected_objects: if get_container(obj): containers.append(obj) + # if bpy.context.active_object: + # if bpy.context.active_object.get('bioxel_layer'): + # if bpy.context.active_object.parent.get('bioxel_container'): + # containers.append(bpy.context.active_object.parent) - return containers + return list(set(containers)) def get_container(current_obj): diff --git a/docs/assets/4d-time.gif b/docs/assets/4d-time.gif new file mode 100644 index 0000000..cc3659d Binary files /dev/null and b/docs/assets/4d-time.gif differ diff --git a/docs/assets/cover.png b/docs/assets/cover.png index 3d99b2e..a740192 100644 Binary files a/docs/assets/cover.png and b/docs/assets/cover.png differ diff --git a/docs/assets/eevee.gif b/docs/assets/eevee.gif new file mode 100644 index 0000000..3debac7 Binary files /dev/null and b/docs/assets/eevee.gif differ diff --git a/docs/assets/gallery.png b/docs/assets/gallery.png index 2c1d3d6..eac61da 100644 Binary files a/docs/assets/gallery.png and 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a/docs/assets/logo.png and b/docs/assets/logo.png differ diff --git a/docs/benchmark.md b/docs/benchmark.md new file mode 100644 index 0000000..e69de29 diff --git a/docs/color.md b/docs/color.md new file mode 100644 index 0000000..a78060c --- /dev/null +++ b/docs/color.md @@ -0,0 +1 @@ +This type of node is responsible for setting the color properties of the shader diff --git a/docs/concept.md b/docs/concept.md new file mode 100644 index 0000000..a44f471 --- /dev/null +++ b/docs/concept.md @@ -0,0 +1,46 @@ +# Concepts & Pipeline + +## Container, Layer, Component + +Bioxel Nodes imports volumetric data and put it into a **Container** as a **Layer**. One container may has more than one layer, and each layer stores the information of different fields under the same location, which is similar to the view layers in map app, except that here it is in 3D space. + +In order to visualize the volumetric data the way we want it to, we need to build renderable objects from layers. We call those objects **Component**. The following diagram shows the relationship of **Container**, **Layer**, and **Component**: + +![alt text](assets/features_concept.png) + +### Container Structure + +In Blender, container structure is like this: + +```bash +Case_0000 # Container +|-- Case_0000_CT # Layer +|-- Case_0000_Label_1 # Layer +`-- Case_0000_Label_2 # Layer +``` + +The container also stores the build process in geometry nodes: + +![alt text](assets/features_container.png) + +### Layer Type +The layer is categorized into these by data type: + +- Scalar +- Label +- Vector (Not implemented yet) +- Color (Not implemented yet) + +## Component Building Pipline + +In order to build a component, the general process is to first use a "Mask Method" node to build the surface of the component based on its layers, and then connect to a "Assign Shader" node to add the physical properties. Finally, if you need to cut the cross-section, then connect to a "Cut" node. The whole process is shown in the following diagram + +![alt text](assets/nodes_concept.png) + +A typical example looks like this: + +![alt text](assets/nodes_example.png) + +The "Mask Method" node tends to be very computationally intensive, and if it consumes too much time, then you can bake it with a "Bake" node after it (but you need to save the Blender file first). + +![alt text](assets/nodes_bake.png) diff --git a/docs/cut.md b/docs/cut.md new file mode 100644 index 0000000..ef6b0ad --- /dev/null +++ b/docs/cut.md @@ -0,0 +1 @@ +This type of node is responsible for cutting components to present cross-section \ No newline at end of file diff --git a/docs/getting-started.md b/docs/getting-started.md deleted file mode 100644 index 5f2f4a4..0000000 --- a/docs/getting-started.md +++ /dev/null @@ -1,72 +0,0 @@ -# Getting Started - -Currently only support Blender 4.0 or above, make sure you have the correct version of Blender. - -## Add-on Installation - -#### For Blender 4.2 or higher - -Download the **Extension** version `BioxelNodes_Extension_{version}.zip` from https://github.com/OmooLab/BioxelNodes/releases/latest -In Blender, Edit > Preferences > Extensions > Install from Disk, select the zip file you just downloaded. - -Thats it! - -> If it cannot be enable, just reboot blender. - -#### For Blender 4.0 or 4.1 - -Download the **Addon** version `BioxelNodes_Addon_{version}.zip` from https://github.com/OmooLab/BioxelNodes/releases/latest -In Blender, Edit > Preferences > Add-ons > Install, select the zip file you just downloaded. - -The add-on requires a third-party python dependency called SimpleITK, click `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 that, click `Reboot Blender` button. - -![dependency](assets/getting-started_dependency.png) - -This step may have failed due to network factors, just click "Set PyPI Mirror" to change the mirror. - -## Prepare Your Data - -First you need to have your volumetric data ready. If not, you can access open research data from list below. - -> Note that just because they are open and available for download does not mean you can use them for anything! Be sure to look at the description of the available scopes from website. - -| Source | Object | -| ------------------------------------------------------------------------------------ | ------------------ | -| [Dryad](https://datadryad.org) | Open Research Data | -| [OpenOrganelle](https://openorganelle.janelia.org/datasets) | Cells | -| [Embodi3D](https://www.embodi3d.com/files/category/37-medical-scans/) | Medical Images | -| [Github](https://github.com/sfikas/medical-imaging-datasets) | Medical Images | -| [NIHR](https://nhsx.github.io/open-source-imaging-data-sets/) | Medical Images | -| [Medical Segmentation Decathlon](http://medicaldecathlon.com/) | Medical Images | -| [Allen Cell Explorer](https://www.allencell.org/3d-cell-viewer.html) | Cells | -| [Visible Human Project](https://www.nlm.nih.gov/research/visible/visible_human.html) | Medical Images | - -## Import Volume Data - -File > Import > Volume Data as Bioxel Layer, select **one** of the .dcm files and click on "Volume Data as Bioxel Layer" (you can also drag one of the .dcm files directly into the 3D viewport to trigger the import) - -![importing](assets/getting-started_importing.png) - -It may take a while to read data. After finishing reading, it will pop up a dialog box. Ignore all the options, just click OK (we will tell about these options later). - -After importing the data, the add-on will automatically add the necessary nodes to build the component. Click on the new created object in outliner, open the geometry nodes panel, set `Threshold` in "Mask by Threshold" node to 200, and then connect a Slime Shader node (Add > Bioxel Nodes > Slime Shader) after it. The node graph should be as following: - -![alt text](assets/getting-started_graph.png) - -and then turned on the cycles rendering to directly see the result. - -![result](assets/getting-started_result.png) - -You can change the "Threshold" to modify the preview model, or change the "Color", "Density" to modify the shader effect. All the parameters are straightforward, you can understand them by changing the values. - -## Share Your File - -The VDB cache and the Bioxel nodes are not reachable to other computers if you don't save them. If you want to give your blender file to someone else, you will need to perform the following steps first: - -1. Save your blender file -2. Click Scene > Bioxels > Save All Bioxels in the properties panel. -3. Click Scene > Custom Nodes > Save All Custom Nodes in the properties panel. - -![alt text](assets/getting-started_share-file.png) - -After that, both the VDB cache and the Bioxel nodes are restored in relative locations. When you share this file with someone, pack the entire directory so that the resources will be not lost. The other person will be able to open it correctly, regardless of whether they have Bioxel Nodes installed or not. diff --git a/docs/features.md b/docs/import.md similarity index 52% rename from docs/features.md rename to docs/import.md index d2f06c5..699fafb 100644 --- a/docs/features.md +++ b/docs/import.md @@ -1,34 +1,3 @@ -# Features & Options - -## Bioxel Design Concept - -According to Bioxel design concept, Bioxel Nodes imports volume data and put it into a **Container** as a **Layer**. One container may has more than one layer, and each layer stores the information of different fields under the same location, which is similar to the view layers in map app, except that here it is in 3D space. In order to render the volume the way we want it to, we need to build renderable objects from layers. We call those objects **Component**. The following diagram shows the relationship of **Container**, **Layer**, and **Component**: - -![alt text](assets/features_concept.png) - -Bioxel Nodes staging the layer as an openvdb file. The process of building from layers to a component is taking place in blender geometry nodes graph with blender native geometry nodes. Therefore, **the blender file works without Bioxel Nodes.** - -## Container Structure - -In Blender, container structure is like this: - -```bash -Case_0000 # Container -|-- Case_0000_CT # Layer -|-- Case_0000_Label_1 # Layer -`-- Case_0000_Label_2 # Layer -``` - -The container also stores the build process in geometry nodes: - -![alt text](assets/features_container.png) - -The layer is categorized into these by data type: - -- Scalar -- Label -- Vector (Not implemented yet) -- Color (Not implemented yet) ## First Time Import Volume Data @@ -69,13 +38,4 @@ A bioxel is like a pixel, the larger the `Bioxel Size`, the lower the resolution ## Adding Volume Data to an existing container In 3D view or outliner panel, select the container and right click, Bioxel Nodes > Add Volume Data to Container. -The import settings are the same as for the first time import. - -## Convert Bioxel Components to Mesh - -In 3D view or outliner panel, select the container and right click, Bioxel Nodes > Bioxel Components To Mesh -Once it has been turned into a mesh model, you can perform any traditional 3D editing operations on it, such as sculpting, boolean, etc. - -## Export Biovel Layer as VDB - -File > Export > Biovel Layer as VDB +The import settings are the same as for the first time import. \ No newline at end of file diff --git a/docs/index.md b/docs/index.md index d3d339d..bb1c1b5 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,23 +1,19 @@ # 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: +Bioxel Nodes is a Blender addon for scientific volumetric data visualization. It using Blender's powerful **Geometry Nodes** and **Cycles** to process and render volumetric data. ![cover](assets/cover.png) -The "Bioxel" in "Bioxel Nodes", is a combination of the words "Bio-" and "Voxel". Bioxel is a voxel that stores biological data. We are developing a toolkit around Bioxel for better biological data visualization. but before its release, we made this Blender version of bioxels toolkit first, in order to let more people to have fun with volumetric data. [Getting Started](https://omoolab.github.io/BioxelNodes/latest/getting-started) +- Fantastic rendering result, also support EEVEE NEXT +- Support multiple formats +- Support 4D volumetric data +- All kinds of cutters +- Simple and powerful nodes +- Based on blender natively, can work without addon. + +**Click [Getting Started](https://omoolab.github.io/BioxelNodes/latest/installation) to begin your journey into visualizing volumetric data!** -## Supported Format +## Support Multiple Formats | Format | EXT | Test | | ------ | ---------------------------------------- | ------- | @@ -28,41 +24,39 @@ The "Bioxel" in "Bioxel Nodes", is a combination of the words "Bio-" and "Voxel" | TIFF | .tif, .TIF, .tiff, .TIFF | βœ… pass | | Nifti | .nia, .nii, .nii.gz, .hdr, .img, .img.gz | βœ… pass | | Nrrd | .nrrd, .nhdr | βœ… pass | -| Meta | .mha, .mhd | yet | | HDF5 | .hdf, .h4, .hdf4, .he2, .h5, .hdf5, .he5 | βœ… 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 +## Support 4D volumetric data -- Sections cannot be generated (will be supported soon) -- Time sequence volume not supported (will be supported soon) +![4d](assets/4d-time.gif) -## To Upgrade Add-on +πŸ₯° 4D volumetric data can also be imported into Blender. -To upgrade from an older version of the add-on to the latest, you need to do the following: +## Support EEVEE NEXT -1. Remove the old version of Bioxel Nodes at Preferences > Add-ons -2. Add the new version and restart Blender. +![eevee](assets/eevee.gif) -It is not support editing the same blender file across add-on versions. In order to make sure that the previous file works properly. You need to save the staged data before upgrading ( read the last section of [Getting Started](https://omoolab.github.io/BioxelNodes/latest/getting-started/#share-your-file) ). +πŸ‘ EEVEE NEXT is absolutely AWESOME! Bioxel Nodes is fully support EEVEE NEXT now! However, there are some limitations: -But even then, there is still no guarantee that the new version of the add-on will work on the old blender file. Therefore, it is highly recommended to open a new blender file to start the creating, not based on the old one. +1. Only one cutter supported. +2. EEVEE result is not that great as Cycles does. -Alternatively, objects from the old file that have nothing to do with Bioxel Nodes could be append to the new blender file. +## Known Limitations -## About EEVEE Render +- Only works with Cycles CPU , Cycles GPU (OptiX), EEVEE +- Section surface cannot be generated when convert to mesh (will be supported soon) -Bioxel Nodes is designed for Cycles Render. However, it does support eevee render partially. "Solid Shader" node and "Volume Shader" node have a toggle called "EEVEE Render". If you want to render Bioxel Component in real-time, turn it on. +## Compatibile to Newer Version -Also, there are some limitations: +**Updating this addon may break old files, so read the following carefully before updating** -1. Only one cutter supported. -2. You cannot use "Color Ramp" over 2 colors. -3. EEVEE Render result is not that great as Cycles does. +Before updating this addon, you need to ask yourself whether this project file will be modified again or not, if it's an archived project file, I would recommend that you run **Bioxel Nodes > Save Staged Data** to make the addon nodes permanent. In this way, there will be no potential problem with the nodes not functioning due to the addon update. + +After the addon update, your old project files may not work either, this may be because you had executed **Save Staged Data**. If so, you need to execute **Bioxel Nodes > Relink Nodes to Addon** to relink them to make sure that the addon's new functionality and the addon nodes are synchronized. + +Also, unlike the newer versions, the older shaders are not based on OSL, so if you find that you can't render volumes, you need to turn on **Open Shading Language (OSL)** in the Render Settings. -> "Volume Shader" node is not work properly in EEVEE Next since 4.2. It is because EEVEE Next is not support attributes from instances of volume shader by now. But the Blender 4.2 docs still say attributes reading is ok, so I suppose this feature will eventually be implemented. +## Roadmap +- Better multi-format import experience +- One-click bake model with texture +- AI Segmentation to Generate Labels \ No newline at end of file diff --git a/docs/installation.md b/docs/installation.md new file mode 100644 index 0000000..9d023b2 --- /dev/null +++ b/docs/installation.md @@ -0,0 +1,27 @@ +# Installation + +> **Currently only support Blender 4.1 or above, make sure you have the correct version of Blender.** + +## For Blender 4.2 or higher + +The most recommended way is to open **Edit > Preferences > Extension**, enter "bio" in the search box and click **Install**. since the addon is quite large (20MB) you may need to wait a while! + +![extension](assets/installation_extension.png) + +Thats it! + +> If it cannot be enable, reboot blender or install again as administrator + +Also, you can do it maually. Download the **Extension** version `BioxelNodes_Extension_{version}.zip` from https://github.com/OmooLab/BioxelNodes/releases/latest +In Blender, **Edit > Preferences > Extensions > Install from Disk**, select the zip file you just downloaded. + +## For Blender 4.1 + +Download the **Addon** version `BioxelNodes_Addon_{version}.zip` from https://github.com/OmooLab/BioxelNodes/releases/latest +In Blender, Edit > Preferences > Add-ons > Install, select the zip file you just downloaded. + +The add-on requires a third-party python dependency called SimpleITK, click `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 that, click `Reboot Blender` button. + +![dependency](assets/installation_dependency.png) + +This step may have failed due to network factors, just click "Set PyPI Mirror" to change the mirror. diff --git a/docs/intergration.md b/docs/intergration.md new file mode 100644 index 0000000..e69de29 diff --git a/docs/mask.md b/docs/mask.md new file mode 100644 index 0000000..c723f85 --- /dev/null +++ b/docs/mask.md @@ -0,0 +1 @@ +This type of node is responsible for culling out the extent of the component that does not need to be rendered, forming the interface between the object and the object, or the surface of the object (i.e., the interface between the object and the air) diff --git a/docs/misc.md b/docs/misc.md deleted file mode 100644 index dbe70f1..0000000 --- a/docs/misc.md +++ /dev/null @@ -1,20 +0,0 @@ -# Future Features - -- Support more volumetric data formats (.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 index 835ab78..cc54ab0 100644 --- a/docs/nodes.md +++ b/docs/nodes.md @@ -1,23 +1,7 @@ # Nodes -## Nodes Design Concept - -In order to build a component, the general process is to first use a "Mask Method" node to build the surface of the component based on its layers, and then connect to a "Assign Shader" node to add the material physical properties. Finally, if you need to cut the cross-section, then connect to a "Cut" node. The whole process is shown in the following diagram - -![alt text](assets/nodes_concept.png) - -A typical example looks like this: - -![alt text](assets/nodes_example.png) - -The "Mask Method" node tends to be very computationally intensive, and if it consumes too much time, then you can bake it with a "Bake" node after it (but you need to save the Blender file first). - -![alt text](assets/nodes_bake.png) - ## Mask Methods -This type of node is responsible for culling out the extent of the component that does not need to be rendered, forming the interface between the object and the object, or the surface of the object (i.e., the interface between the object and the air) - ### ⬆️ Mask by Threshold
@@ -91,8 +75,6 @@ This type of node is responsible for culling out the extent of the component tha ## Shaders -This type of node is responsible for setting material physical properties to the component to reflect the differences in rendering effects of different components. - ### πŸ₯š Solid Shader
@@ -192,8 +174,6 @@ This type of node is responsible for setting material physical properties to the ## Cutters -This type of node is responsible for cutting components to present cross-section - ### πŸͺš Cut
@@ -212,25 +192,6 @@ This type of node is responsible for cutting components to present cross-section
-### πŸ§€ Plane Cutter - -
- -- ![alt text](assets/nodes_plane-cutter.png) - -- Flat plane cutter, cuts off above Z-axis in local. - - *** - - Node Parameter: - - - **Origin**, _plane cutter position_ - - **Direction**, _plane cutter orientation_ - - Guide - - **Show**, _show the cutter guide_ - - **Scale**, _scale the cutter guide_ - -
### πŸ§€ Plane Object Cutter @@ -253,8 +214,6 @@ This type of node is responsible for cutting components to present cross-section ## Colors -This type of node is responsible for setting the color properties of the shader - ### 🎨 Color Presents
diff --git a/docs/prepare_data.md b/docs/prepare_data.md new file mode 100644 index 0000000..76409e8 --- /dev/null +++ b/docs/prepare_data.md @@ -0,0 +1,41 @@ +# Prepare Your Data + +## Support Formats + +First thing first, you need to get your volumetric data ready in disk. Bioxel Nodes is developed based on Simple ITK, so theoretically all formats supported by Simple ITK are supported by the addon. If your data is not in the support list, you may do the data conversion first. + +| Format | EXT | Test | +| ------ | ---------------------------------------- | ------- | +| DICOM | .dcm, .DICOM | βœ… pass | +| BMP | .bmp, .BMP | βœ… pass | +| JPEG | .jpg, .JPG, .jpeg, .JPEG | βœ… pass | +| PNG | .png, .PNG | βœ… pass | +| TIFF | .tif, .TIF, .tiff, .TIFF | βœ… pass | +| Nifti | .nia, .nii, .nii.gz, .hdr, .img, .img.gz | βœ… pass | +| Nrrd | .nrrd, .nhdr | βœ… pass | +| Meta | .mha, .mhd | yet | +| HDF5 | .hdf, .h4, .hdf4, .he2, .h5, .hdf5, .he5 | βœ… 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 | + +## Download Data from Internet + +If you don't have any volumetric data, you can access open research data from list below. + +> Note that just because they are open and available for download does not mean you can use them for anything! Be sure to look at the description of the available scopes from website. + +| Source | Object | +| ------------------------------------------------------------------------------------ | ------------------ | +| [MorphoSource](https://www.morphosource.org/) | Open Research Data | +| [Dryad](https://datadryad.org) | Open Research Data | +| [OpenOrganelle](https://openorganelle.janelia.org/datasets) | Cells | +| [Embodi3D](https://www.embodi3d.com/files/category/37-medical-scans/) | Medical Images | +| [Github](https://github.com/sfikas/medical-imaging-datasets) | Medical Images | +| [NIHR](https://nhsx.github.io/open-source-imaging-data-sets/) | Medical Images | +| [Medical Segmentation Decathlon](http://medicaldecathlon.com/) | Medical Images | +| [Allen Cell Explorer](https://www.allencell.org/3d-cell-viewer.html) | Cells | +| [Visible Human Project](https://www.nlm.nih.gov/research/visible/visible_human.html) | Medical Images | diff --git a/docs/render.md b/docs/render.md new file mode 100644 index 0000000..e69de29 diff --git a/docs/shader.md b/docs/shader.md new file mode 100644 index 0000000..812e94b --- /dev/null +++ b/docs/shader.md @@ -0,0 +1 @@ +This type of node is responsible for setting material physical properties to the component to reflect the differences in rendering effects of different components. \ No newline at end of file diff --git a/docs/step_by_step.md b/docs/step_by_step.md new file mode 100644 index 0000000..c6ca945 --- /dev/null +++ b/docs/step_by_step.md @@ -0,0 +1,54 @@ +# Step by Step + +## 1. Import Volumetric Data + +**Bioxel Nodes > Import Volumetric Data (Init) > as Scalar**, select the data file, click on **Import as Scalar**. If the data is a sequence of files in directory, just pick **one** file in that directory, not the whole directory or multiple selection of files. + +> you can also drag one of the data file directly into the 3D viewport to trigger the importing + +![importing](assets/getting-started_importing.png) + +It may take a while to read data. After finishing reading, it will pop up a dialog box. Ignore all the options, just click OK (we will talk about them later). + +After the importing, the add-on will automatically add the necessary nodes to build the preview. + +![masking](assets/getting-started_masking.png) + +If there is nothing in the bbox wireframe, select the wireframe in 3D viewport, open the geometry nodes panel, set **Threshold** in the node lower to modify the preview. + +## 2. Shading the Structure + +The only node "Scalar" is responsible for mask out the unwanted area and generate the structure surface. You need to assign a shader to truly see the structure, connect a **Slime Shader** node (**Add > Bioxel Nodes > Shaders > Slime Shader**) after it. Turned on the cycles rendering to see the result. + +![shading](assets/getting-started_shading.png) + +You may change the **Color**, **Density** to modify the shader effect. All the parameters are straightforward, you can understand them by changing their values. + +## 3. Cut to Cross-section + +We often need to cut the structure to see the inside of the volumetric data. With Bioxel Nodes, it can be done by one click: select the structure in 3D viewport, right click, **Bioxel Nodes > Add a Plane Cutter** +. The add-on will add a cut node and a cutter object node to the node graph, which are responsible for the cutting process. + +![cutting](assets/getting-started_cutting.png) + +> Change the shader from **Slime** to **Universal** to render the cross-section. But it will increase rendering time + +## 4. Save Staged Data (Optional) + +The VDB cache and the custom nodes are not reachable to other computers if you don't save them. Those staged data should be saved, If you want to give your blender file to someone else, or you want to archive your blender file. + +Save your blender file, then just click **Bioxel Nodes > Save Staged Data** + +![save staged data](assets/getting-started_save_staged_data.png) + +Just click **OK**, after that, both the VDB cache and the custom nodes are restored in relative locations. When you share this file with someone, pack the entire directory so that the resources will be not lost. The other person will be able to open it correctly, regardless of whether they have Bioxel Nodes installed or not. + +## 5. Convert to Editable Mesh (Optional) + +If you want digital sculpting, 3D printing, exporting to game engine, you should convert to editable mesh first. + +Select the wireframe in 3D viewport, right click **Bioxel Nodes > Pick Mesh**. + +![to mesh](assets/getting-started_convert_to_mesh.png) + +It will create a new object with geometry nodes to refer the mesh. You can apply the geometry node to break the connection. diff --git a/docs/terms.md b/docs/terms.md new file mode 100644 index 0000000..3064394 --- /dev/null +++ b/docs/terms.md @@ -0,0 +1,7 @@ +# Terms + +### 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. diff --git a/extension/blender_manifest.toml b/extension/blender_manifest.toml index 77857e3..74ffae5 100644 --- a/extension/blender_manifest.toml +++ b/extension/blender_manifest.toml @@ -3,7 +3,7 @@ schema_version = "1.0.0" # Example of manifest file for a Blender extension # Change the values according to your extension id = "bioxelnodes" -version = "0.2.6" +version = "0.2.7" name = "Bioxel Nodes" tagline = "For scientific volumetric data visualization in Blender" maintainer = "Ma Nan " diff --git a/mkdocs.yml b/mkdocs.yml index 24e9ad3..724a76d 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -1,4 +1,4 @@ -site_name: Bioxel Nodes Docs +site_name: Bioxel Nodes Handbook site_url: https://omoolab.github.io/BioxelNodes/ site_author: OmooLab site_description: Bioxel Nodes is a Blender add-on for scientific volumetric data visualization. @@ -7,15 +7,28 @@ repo_name: OmooLab/BioxelNodes repo_url: https://github.com/OmooLab/BioxelNodes nav: - - BioxelNodes: - - index.md - - Getting Started: getting-started.md - - Features & Options: features.md + - index.md + - Getting Started: + - Installation: installation.md + - Prepare Your Data: prepare_data.md + - Step by Step: step_by_step.md + - Concepts & Pipeline: concept.md + - Visualizating any Bio-structure: + - Import & Preprocess: import.md + - Mask Methods: mask.md + - Assgin a Shader: shader.md + - Cut the Component: cut.md + - Set Colors: color.md + - Integration into Other Pipeline: intergration.md + - Render Tips: render.md + - Reference: + - Terms: terms.md - Nodes: nodes.md - - Future Features: misc.md + - Benchmark: benchmark.md theme: name: material + favicon: assets/logo.png logo: assets/logo.png language: en font: diff --git a/pyproject.toml b/pyproject.toml index 7ac030e..3af895f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "bioxelnodes" -version = "0.2.6" +version = "0.2.7" description = "" authors = ["Ma Nan "] license = "MIT"