Merge pull request #33 from OmooLab/feature/dev

chore: update version

.github/workflows/upload-assets.yml

@@ -88,7 +88,15 @@ jobs:
           python-version: 3.11
       - name: Zip Extension
         run: |
-          pip download SimpleITK==2.3.1 --dest bioxelnodes/wheels --only-binary=:all: --python-version=3.11 --platform=win_amd64
+          pip download SimpleITK==2.3.1 --dest wheels --only-binary=:all: --python-version=3.11 --platform=win_amd64
+          pip download pyometiff==1.0.0 --dest wheels --only-binary=:all: --python-version=3.11 --platform=win_amd64
+          pip download mrcfile==1.5.1 --dest wheels --only-binary=:all: --python-version=3.11 --platform=win_amd64
+          mkdir bioxelnodes/wheels
+          cp wheels/SimpleITK-2.3.1-cp311-cp311-win_amd64.whl bioxelnodes/wheels/SimpleITK-2.3.1-cp311-cp311-win_amd64.whl
+          cp wheels/lxml-5.2.2-cp311-cp311-win_amd64.whl bioxelnodes/wheels/lxml-5.2.2-cp311-cp311-win_amd64.whl
+          cp wheels/tifffile-2024.7.21-py3-none-any.whl bioxelnodes/wheels/tifffile-2024.7.21-py3-none-any.whl
+          cp wheels/pyometiff-1.0.0-py3-none-any.whl bioxelnodes/wheels/pyometiff-1.0.0-py3-none-any.whl
+          cp wheels/mrcfile-1.5.1-py2.py3-none-any.whl bioxelnodes/wheels/mrcfile-1.5.1-py2.py3-none-any.whl
           rm -r bioxelnodes/externalpackage
           cp extension/__init__.py bioxelnodes/__init__.py
           cp extension/preferences.py bioxelnodes/preferences.py

README.md

@@ -2,29 +2,33 @@
 
 # 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)
+[![For Blender](https://img.shields.io/badge/Blender-orange?style=for-the-badge&logo=blender&logoColor=white&color=black)](https://blender.org/)
+![GitHub License](https://img.shields.io/github/license/OmooLab/BioxelNodes?style=for-the-badge&labelColor=black)
+![GitHub Release](https://img.shields.io/github/v/release/OmooLab/BioxelNodes?style=for-the-badge&labelColor=black)
+![GitHub Repo stars](https://img.shields.io/github/stars/OmooLab/BioxelNodes?style=for-the-badge&labelColor=black)
+
+[![Discord](https://img.shields.io/discord/1265129134397587457?style=for-the-badge&logo=discord&label=Discord&labelColor=white&color=black)](https://discord.gg/pYkNyq2TjE)
 
 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)
 
--   Fantastic rendering result, also support EEVEE NEXT
--   Support multiple formats
--   Support 4D volumetric data
--   All kinds of cutters
--   Simple and powerful nodes
+-   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!**
+**Read the [getting started](https://omoolab.github.io/BioxelNodes/latest/installation) to begin your journey into visualizing volumetric data!**
+
+Welcome to our [discord server](https://discord.gg/pYkNyq2TjE), if you have any problems with this add-on.
 
 ## Support Multiple Formats
 
 | Format | EXT                                      | Test    |
 | ------ | ---------------------------------------- | ------- |
-| DICOM  | .dcm, .DICOM                             | ✅ pass |
+| DICOM  | .dcm, .DCM, .DICOM, .ima, .IMA           | ✅ pass |
 | BMP    | .bmp, .BMP                               | ✅ pass |
 | JPEG   | .jpg, .JPG, .jpeg, .JPEG                 | ✅ pass |
 | PNG    | .png, .PNG                               | ✅ pass |
@@ -32,6 +36,8 @@ Bioxel Nodes is a Blender addon for scientific volumetric data visualization. It
 | Nifti  | .nia, .nii, .nii.gz, .hdr, .img, .img.gz | ✅ pass |
 | Nrrd   | .nrrd, .nhdr                             | ✅ pass |
 | HDF5   | .hdf, .h4, .hdf4, .he2, .h5, .hdf5, .he5 | ✅ pass |
+| OME    | .ome.tiff, .ome.tif                      | ✅ pass |
+| MRC    | .mrc, .mrc.gz, .map, .map.gz             | ✅ pass |
 
 ## Support 4D volumetric data
 
@@ -53,7 +59,7 @@ Bioxel Nodes is a Blender addon for scientific volumetric data visualization. It
 -   Only works with Cycles CPU , Cycles GPU (OptiX), EEVEE
 -   Section surface cannot be generated when convert to mesh (will be supported soon)
 
-## Compatibile to Newer Version
+## Compatible to Newer Version
 
 **Updating this addon may break old files, so read the following carefully before updating**
 

bioxelnodes/__init__.py

@@ -9,7 +9,7 @@ bl_info = {
     "author": "Ma Nan",
     "description": "",
     "blender": (4, 1, 0),
-    "version": (0, 2, 7),
+    "version": (0, 2, 9),
     "location": "File -> Import",
     "warning": "",
     "category": "Node"
@@ -20,6 +20,8 @@ auto_load.init()
 
 def register():
     auto_load.register()
+    bpy.types.WindowManager.bioxelnodes_progress_factor = bpy.props.FloatProperty()
+    bpy.types.WindowManager.bioxelnodes_progress_text = bpy.props.StringProperty()
     menus.add()
 
 

bioxelnodes/exceptions.py

@@ -0,0 +1,4 @@
+class CancelledByUser(Exception):
+    def __init__(self):
+        message = 'Cancelled by user'
+        super().__init__(message)

bioxelnodes/menus.py

@@ -3,7 +3,7 @@ import bpy
 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 .io import ExportVolumetricData, ImportAsLabelLayer, ImportAsScalarLayer
 from .save import CleanAllCaches, ReLinkNodes, SaveLayers, SaveStagedData
 
 
@@ -115,7 +115,7 @@ class BioxelNodesOutlinerMenu(bpy.types.Menu):
         layout.operator(FillByLabel.bl_idname)
         layout.operator(CombineLabels.bl_idname)
         layout.separator()
-        layout.operator(ExportVolumeData.bl_idname)
+        layout.operator(ExportVolumetricData.bl_idname)
 
 
 def TOPBAR_FILE_IMPORT(self, context):
@@ -131,7 +131,7 @@ def TOPBAR_FILE_IMPORT(self, context):
 def TOPBAR_FILE_EXPORT(self, context):
     layout = self.layout
     layout.separator()
-    layout.operator(ExportVolumeData.bl_idname,
+    layout.operator(ExportVolumetricData.bl_idname,
                     text="Bioxel Layer (.vdb)")
 
 

bioxelnodes/operators.py

@@ -89,8 +89,8 @@ def deep_copy_layer(vdb_path, base_layer, name):
     copyed_layer.hide_select = True
     copyed_layer.hide_render = True
     copyed_layer.hide_viewport = True
-    copyed_layer.data.display.use_slice = True
-    copyed_layer.data.display.density = 1e-05
+    # copyed_layer.data.display.use_slice = True
+    # copyed_layer.data.display.density = 1e-05
 
     copyed_layer['bioxel_layer'] = True
     copyed_layer['bioxel_layer_type'] = base_layer['bioxel_layer_type']
@@ -366,7 +366,7 @@ class FillByThreshold(bpy.types.Operator):
     def invoke(self, context, event):
         base_layer = get_layer(bpy.context.active_object)
         scalar_min = get_layer_meta(base_layer, "Scalar Min")
-        self.fill_value = scalar_min
+        self.fill_value = min(scalar_min,0)
         context.window_manager.invoke_props_dialog(self, width=400)
         return {'RUNNING_MODAL'}
 
@@ -449,7 +449,7 @@ class FillByRange(bpy.types.Operator):
     def invoke(self, context, event):
         base_layer = get_layer(bpy.context.active_object)
         scalar_min = get_layer_meta(base_layer, "Scalar Min")
-        self.fill_value = scalar_min
+        self.fill_value = min(scalar_min,0)
         context.window_manager.invoke_props_dialog(self, width=400)
         return {'RUNNING_MODAL'}
 
@@ -533,7 +533,7 @@ class FillByLabel(bpy.types.Operator):
     def invoke(self, context, event):
         base_layer = get_layer(bpy.context.active_object)
         scalar_min = get_layer_meta(base_layer, "Scalar Min")
-        self.fill_value = scalar_min
+        self.fill_value = min(scalar_min,0)
         context.window_manager.invoke_props_dialog(self, width=400)
         return {'RUNNING_MODAL'}
 

bioxelnodes/parse.py

@@ -0,0 +1,408 @@
+from pathlib import Path
+import numpy as np
+
+from .exceptions import CancelledByUser
+from .utils import get_text_index_str
+
+try:
+    import SimpleITK as sitk
+    from pyometiff import OMETIFFReader
+    import mrcfile
+except:
+    ...
+
+"""
+Convert any volumetric data to 3D numpy array with order TXYZC
+"""
+
+SUPPORT_EXTS = ['', '.dcm', '.DCM', '.DICOM', '.ima', '.IMA',
+                '.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',
+                '.ome.tiff', '.ome.tif',
+                '.mrc', '.mrc.gz', '.map', '.map.gz']
+
+OME_EXTS = ['.ome.tiff', '.ome.tif',
+            '.tif', '.TIF', '.tiff', '.TIFF']
+
+MRC_EXTS = ['.mrc', '.mrc.gz', '.map', '.map.gz']
+
+SEQUENCE_EXTS = ['.bmp', '.BMP',
+                 '.jpg', '.JPG', '.jpeg', '.JPEG',
+                 '.tif', '.TIF', '.tiff', '.TIFF',
+                 '.png', '.PNG']
+
+DICOM_EXTS = ['', '.dcm', '.DCM', '.DICOM', '.ima', '.IMA']
+
+FH_EXTS = ['', '.dcm', '.DCM', '.DICOM', '.ima', '.IMA',
+           '.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_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"
+    elif file_path.name.endswith(".ome.tiff"):
+        return ".ome.tiff"
+    elif file_path.name.endswith(".ome.tif"):
+        return ".ome.tif"
+    elif file_path.name.endswith(".mrc.gz"):
+        return ".mrc.gz"
+    elif file_path.name.endswith(".map.gz"):
+        return ".map.gz"
+    else:
+        return file_path.suffix
+
+
+def get_sequence_name(filepath: str) -> str:
+    ext = get_ext(filepath)
+    filename = Path(filepath).name.removesuffix(ext)
+    index: str = get_text_index_str(filename)
+    return filename.removesuffix(index)
+
+
+def get_sequence_index(filepath: str) -> int:
+    ext = get_ext(filepath)
+    filename = Path(filepath).name.removesuffix(ext)
+    index: str = get_text_index_str(filename)
+    return int(index) if index else 0
+
+
+def collect_sequence(filepath: str):
+    file_path = Path(filepath).resolve()
+
+    files = list(file_path.parent.iterdir())
+    file_dict = {}
+    for file in files:
+        if file.is_file() \
+                and get_ext(file_path) == get_ext(file) \
+                and get_sequence_name(file_path) == get_sequence_name(file):
+            file_dict[get_sequence_index(file)] = file
+
+    for key in file_dict.copy().keys():
+        if not file_dict.get(key+1) \
+                and not file_dict.get(key-1):
+            del file_dict[key]
+
+    file_dict = dict(sorted(file_dict.items()))
+    sequence = [str(f) for f in file_dict.values()]
+
+    if len(sequence) == 0:
+        sequence = [str(file_path)]
+
+    return sequence
+
+
+def parse_volumetric_data(filepath: str, series_id="", progress_callback=None):
+    """Parse any volumetric data to numpy with shap (T,X,Y,Z,C)
+
+    Args:
+        filepath (str): file path
+        series_id (str, optional): DICOM series id. Defaults to "".
+
+    Returns:
+        _type_: _description_
+    """
+    ext = get_ext(filepath)
+
+    if progress_callback:
+        progressing = progress_callback(0, "Reading the Data...")
+        if not progressing:
+            raise CancelledByUser
+
+    is_sequence = False
+    if ext in SEQUENCE_EXTS:
+        sequence = collect_sequence(filepath)
+        if len(sequence) > 1:
+            is_sequence = True
+
+    volume = None
+
+    # Parsing with mrcfile
+    if volume is None and ext in MRC_EXTS and not is_sequence:
+        print("Parsing with mrcfile...")
+        # TODO: much to do with mrc
+        with mrcfile.open(filepath) as mrc:
+            volume = mrc.data
+            # mrc.print_header()
+            # print(volume.shape)
+            # print(mrc.voxel_size)
+
+            if mrc.is_single_image():
+                volume = np.expand_dims(volume, axis=0)  # expend frame
+                volume = np.expand_dims(volume, axis=-1)  # expend Z
+                volume = np.expand_dims(volume, axis=-1)  # expend channel
+
+            elif mrc.is_image_stack():
+                volume = np.expand_dims(volume, axis=-1)  # expend Z
+                volume = np.expand_dims(volume, axis=-1)  # expend channel
+
+            elif mrc.is_volume():
+                volume = np.expand_dims(volume, axis=0)  # expend frame
+                volume = np.expand_dims(volume, axis=-1)  # expend channel
+
+            elif mrc.is_volume_stack():
+                volume = np.expand_dims(volume, axis=-1)  # expend channel
+            name = Path(filepath).name.removesuffix(ext).replace(" ", "-")
+            shape = volume.shape[1:4]
+            spacing = (mrc.voxel_size.x, mrc.voxel_size.y, mrc.voxel_size.z)
+
+            meta = {
+                "name": name,
+                "description": "",
+                "shape": shape,
+                "spacing": spacing,
+                "origin": (0, 0, 0),
+                "direction": (1, 0, 0, 0, 1, 0, 0, 0, 1),
+                "frame_count": volume.shape[0],
+                "channel_count": volume.shape[-1],
+                "is_oriented": False
+            }
+
+    # Parsing with OMETIFFReader
+    if volume is None and ext in OME_EXTS and not is_sequence:
+        print("Parsing with OMETIFFReader...")
+        reader = OMETIFFReader(fpath=filepath)
+        ome_volume, metadata, xml_metadata = reader.read()
+
+        if progress_callback:
+            progressing = progress_callback(0.5, "Transpose to 'TXYZC'...")
+            if not progressing:
+                raise CancelledByUser
+
+        try:
+            # print(ome_volume.shape)
+            # for key in metadata:
+            #     print(f"{key},{metadata[key]}")
+            ome_order = metadata['DimOrder BF Array']
+            if ome_volume.ndim == 2:
+                ome_order = ome_order.replace("T", "")\
+                    .replace("C", "").replace("Z", "")
+                bioxel_order = (ome_order.index('X'),
+                                ome_order.index('Y'))
+                volume = np.transpose(ome_volume, bioxel_order)
+                volume = np.expand_dims(volume, axis=0)  # expend frame
+                volume = np.expand_dims(volume, axis=-1)  # expend Z
+                volume = np.expand_dims(volume, axis=-1)  # expend channel
+
+            elif ome_volume.ndim == 3:
+                # -> XYZC
+                ome_order = ome_order.replace("T", "").replace("C", "")
+                bioxel_order = (ome_order.index('X'),
+                                ome_order.index('Y'),
+                                ome_order.index('Z'))
+                volume = np.transpose(ome_volume, bioxel_order)
+                volume = np.expand_dims(volume, axis=0)  # expend frame
+                volume = np.expand_dims(volume, axis=-1)  # expend channel
+            elif ome_volume.ndim == 4:
+                # -> XYZC
+                ome_order = ome_order.replace("T", "")
+                bioxel_order = (ome_order.index('X'),
+                                ome_order.index('Y'),
+                                ome_order.index('Z'),
+                                ome_order.index('C'))
+                volume = np.transpose(ome_volume, bioxel_order)
+                volume = np.expand_dims(volume, axis=0)  # expend frame
+            elif ome_volume.ndim == 5:
+                # -> TXYZC
+                bioxel_order = (ome_order.index('T'),
+                                ome_order.index('X'),
+                                ome_order.index('Y'),
+                                ome_order.index('Z'),
+                                ome_order.index('C'))
+                volume = np.transpose(ome_volume, bioxel_order)
+
+            shape = volume.shape[1:4]
+
+            try:
+                spacing = (metadata['PhysicalSizeX'],
+                           metadata['PhysicalSizeY'],
+                           metadata['PhysicalSizeZ'])
+            except:
+                spacing = (1, 1, 1)
+
+            name = Path(filepath).name.removesuffix(ext).replace(" ", "-")
+            meta = {
+                "name": name,
+                "description": "",
+                "shape": shape,
+                "spacing": spacing,
+                "origin": (0, 0, 0),
+                "direction": (1, 0, 0, 0, 1, 0, 0, 0, 1),
+                "frame_count": volume.shape[0],
+                "channel_count": volume.shape[-1],
+                "is_oriented": False
+            }
+        except:
+            ...
+
+    # Parsing with SimpleITK
+    if volume is None:
+        print("Parsing with SimpleITK...")
+        if ext in DICOM_EXTS:
+            dir_path = Path(filepath).resolve().parent
+            reader = sitk.ImageSeriesReader()
+            reader.MetaDataDictionaryArrayUpdateOn()
+            reader.LoadPrivateTagsOn()
+            series_files = reader.GetGDCMSeriesFileNames(
+                str(dir_path), series_id)
+            reader.SetFileNames(series_files)
+
+            itk_volume = reader.Execute()
+            # for k in reader.GetMetaDataKeys(0):
+            #     v = reader.GetMetaData(0, k)
+            #     print(f'({k}) = = "{v}"')
+
+            def get_meta(key):
+                try:
+                    stirng = reader.GetMetaData(0, key).removesuffix(" ")
+                    if stirng in ["No study description",
+                                  "No series description"]:
+                        return None
+                    else:
+                        return stirng
+                except:
+                    return None
+
+            study_description = get_meta("0008|1030")
+            series_description = get_meta("0008|103e")
+            series_modality = get_meta("0008|0060")
+
+            name = study_description or dir_path.name
+            if series_description and series_modality:
+                description = f"{series_description}-{series_modality}"
+            elif series_description:
+                description = series_description
+            elif series_modality:
+                description = series_modality
+            else:
+                description = ""
+
+            name = name.replace(" ", "-")
+            description = description.replace(" ", "-")
+
+        elif ext in SEQUENCE_EXTS and is_sequence:
+            try:
+                itk_volume = sitk.ReadImage(sequence)
+                name = get_sequence_name(filepath).replace(" ", "-")
+                description = ""
+            except RuntimeError as e:
+                raise e
+        else:
+            itk_volume = sitk.ReadImage(filepath)
+            name = Path(filepath).name.removesuffix(ext).replace(" ", "-")
+            description = ""
+
+        # for key in itk_volume.GetMetaDataKeys():
+        #     print(f"{key},{itk_volume.GetMetaData(key)}")
+
+        if progress_callback:
+            progressing = progress_callback(0.5, "Transpose to 'TXYZC'...")
+            if not progressing:
+                raise CancelledByUser
+
+        if itk_volume.GetDimension() == 2:
+            volume = sitk.GetArrayFromImage(itk_volume)
+
+            if volume.ndim == 3:
+                volume = np.transpose(volume, (1, 0, 2))
+
+                volume = np.expand_dims(volume, axis=-2)  # expend Z
+            else:
+                volume = np.transpose(volume)
+                volume = np.expand_dims(volume, axis=-1)  # expend Z
+                volume = np.expand_dims(volume, axis=-1)  # expend channel
+
+            volume = np.expand_dims(volume, axis=0)  # expend frame
+
+            meta = {
+                "name": name,
+                "description": description,
+                "shape": volume.shape[1:4],
+                "spacing": (1, 1, 1),
+                "origin": (0, 0, 0),
+                "direction": (1, 0, 0, 0, 1, 0, 0, 0, 1),
+                "frame_count": 1,
+                "channel_count": volume.shape[-1],
+                "is_oriented": False
+            }
+
+        elif itk_volume.GetDimension() == 3:
+            itk_volume = sitk.DICOMOrient(itk_volume, 'RAS')
+
+            volume = sitk.GetArrayFromImage(itk_volume)
+
+            # 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)  # expend channel
+
+            volume = np.expand_dims(volume, axis=0)  # expend frame
+
+            meta = {
+                "name": name,
+                "description": description,
+                "shape": tuple(itk_volume.GetSize()),
+                "spacing": tuple(itk_volume.GetSpacing()),
+                "origin": tuple(itk_volume.GetOrigin()),
+                "direction": tuple(itk_volume.GetDirection()),
+                "frame_count": 1,
+                "channel_count": volume.shape[-1],
+                "is_oriented": True
+            }
+
+        elif itk_volume.GetDimension() == 4:
+            # FIXME: not sure...
+            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())
+
+            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)
+
+            meta = {
+                "name": name,
+                "description": description,
+                "shape": tuple(itk_volume.GetSize()[:3]),
+                "spacing": tuple(itk_volume.GetSpacing()[:3]),
+                "origin": tuple(itk_volume.GetOrigin()[:3]),
+                "direction": direction,
+                "frame_count": volume.shape[0],
+                "channel_count": volume.shape[-1],
+                "is_oriented": False
+            }
+
+    return volume, meta

bioxelnodes/requirements.txt

@@ -1 +1,3 @@
 SimpleITK==2.3.1     # Insight Segmentation and Registration Toolkit.
+pyometiff==1.0.0     # .ome.tiff
+mrcfile==1.5.1       # .map

bioxelnodes/utils.py

@@ -72,12 +72,19 @@ def get_nodes_by_type(node_group, type_name: str):
     return [node for node in node_group.nodes if get_node_type(node) == type_name]
 
 
-def show_message(message="", title="Message Box", icon='INFO'):
+def progress_bar(self, context):
+    row = self.layout.row()
+    row.progress(
+        factor=context.window_manager.bioxelnodes_progress_factor,
+        type="BAR",
+        text=context.window_manager.bioxelnodes_progress_text
+    )
+    row.scale_x = 2
 
-    def draw(self, context):
-        self.layout.label(text=message)
 
-    bpy.context.window_manager.popup_menu(draw, title=title, icon=icon)
+def progress_update(context, factor, text=""):
+    context.window_manager.bioxelnodes_progress_factor = factor
+    context.window_manager.bioxelnodes_progress_text = text
 
 
 def calc_bbox_verts(origin, size):
@@ -157,7 +164,7 @@ def save_vdb(grids, context):
     cache_dir.mkdir(parents=True, exist_ok=True)
 
     vdb_path = Path(cache_dir, f"{uuid4()}.vdb")
-    print(f"Storing the VDB file ({str(vdb_path)})...")
+    # print(f"Storing the VDB file ({str(vdb_path)})...")
     vdb.write(str(vdb_path), grids=grids)
 
     return vdb_path
@@ -174,7 +181,7 @@ def save_vdbs(grids_sequence, context):
     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)})...")
+        # print(f"Storing the VDB file ({str(vdb_path)})...")
         vdb.write(str(vdb_path), grids=grids)
         vdb_paths.append(vdb_path)
 

docs/index.md

@@ -1,23 +1,34 @@
+[中文文档](https://uj6xfhbzp0.feishu.cn/wiki/Qx3VwHuNPimeI8kr6nDcvl1DnHf?from=from_copylink)
+
 # Bioxel Nodes
 
+[![For Blender](https://img.shields.io/badge/Blender-orange?style=for-the-badge&logo=blender&logoColor=white&color=black)](https://blender.org/)
+![GitHub License](https://img.shields.io/github/license/OmooLab/BioxelNodes?style=for-the-badge&labelColor=black)
+![GitHub Release](https://img.shields.io/github/v/release/OmooLab/BioxelNodes?style=for-the-badge&labelColor=black)
+![GitHub Repo stars](https://img.shields.io/github/stars/OmooLab/BioxelNodes?style=for-the-badge&labelColor=black)
+
+[![Discord](https://img.shields.io/discord/1265129134397587457?style=for-the-badge&logo=discord&label=Discord&labelColor=white&color=black)](https://discord.gg/pYkNyq2TjE)
+
 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)
+![cover](https://omoolab.github.io/BioxelNodes/latest/assets/cover.png)
 
--   Fantastic rendering result, also support EEVEE NEXT
--   Support multiple formats
--   Support 4D volumetric data
--   All kinds of cutters
--   Simple and powerful nodes
+-   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!**
+**Read the [getting started](https://omoolab.github.io/BioxelNodes/latest/installation) to begin your journey into visualizing volumetric data!**
+
+Welcome to our [discord server](https://discord.gg/pYkNyq2TjE), if you have any problems with this add-on.
 
 ## Support Multiple Formats
 
 | Format | EXT                                      | Test    |
 | ------ | ---------------------------------------- | ------- |
-| DICOM  | .dcm, .DICOM                             | ✅ pass |
+| DICOM  | .dcm, .DCM, .DICOM, .ima, .IMA           | ✅ pass |
 | BMP    | .bmp, .BMP                               | ✅ pass |
 | JPEG   | .jpg, .JPG, .jpeg, .JPEG                 | ✅ pass |
 | PNG    | .png, .PNG                               | ✅ pass |
@@ -25,6 +36,8 @@ Bioxel Nodes is a Blender addon for scientific volumetric data visualization. It
 | Nifti  | .nia, .nii, .nii.gz, .hdr, .img, .img.gz | ✅ pass |
 | Nrrd   | .nrrd, .nhdr                             | ✅ pass |
 | HDF5   | .hdf, .h4, .hdf4, .he2, .h5, .hdf5, .he5 | ✅ pass |
+| OME    | .ome.tiff, .ome.tif                      | ✅ pass |
+| MRC    | .mrc, .mrc.gz, .map, .map.gz             | ✅ pass |
 
 ## Support 4D volumetric data
 
@@ -46,7 +59,7 @@ Bioxel Nodes is a Blender addon for scientific volumetric data visualization. It
 -   Only works with Cycles CPU , Cycles GPU (OptiX), EEVEE
 -   Section surface cannot be generated when convert to mesh (will be supported soon)
 
-## Compatibile to Newer Version
+## Compatible to Newer Version
 
 **Updating this addon may break old files, so read the following carefully before updating**
 
@@ -57,6 +70,7 @@ After the addon update, your old project files may not work either, this may be
 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
+
 -   Better multi-format import experience
 -   One-click bake model with texture
 -   AI Segmentation to Generate Labels

docs/prepare_data.md

@@ -6,7 +6,7 @@ First thing first, you need to get your volumetric data ready in disk. Bioxel No
 
 | Format | EXT                                      | Test    |
 | ------ | ---------------------------------------- | ------- |
-| DICOM  | .dcm, .DICOM                             | ✅ pass |
+| DICOM  | .dcm, .DCM, .DICOM, .ima, .IMA           | ✅ pass |
 | BMP    | .bmp, .BMP                               | ✅ pass |
 | JPEG   | .jpg, .JPG, .jpeg, .JPEG                 | ✅ pass |
 | PNG    | .png, .PNG                               | ✅ pass |
@@ -21,6 +21,8 @@ First thing first, you need to get your volumetric data ready in disk. Bioxel No
 | LSM    | .lsm, .LSM                               | yet     |
 | MINC   | .mnc, .MNC                               | yet     |
 | MRC    | .mrc, .rec                               | yet     |
+| OME    | .ome.tiff, .ome.tif                      | ✅ pass |
+| MRC    | .mrc, .mrc.gz, .map, .map.gz             | ✅ pass |
 
 ## Download Data from Internet
 
@@ -32,10 +34,12 @@ If you don't have any volumetric data, you can access open research data from li
 | ------------------------------------------------------------------------------------ | ------------------ |
 | [MorphoSource](https://www.morphosource.org/)                                        | Open Research Data |
 | [Dryad](https://datadryad.org)                                                       | Open Research Data |
+| [Cell Image Library](http://cellimagelibrary.org/home)                               | Cells              |
 | [OpenOrganelle](https://openorganelle.janelia.org/datasets)                          | Cells              |
+| [Allen Cell Explorer](https://www.allencell.org/3d-cell-viewer.html)                 | Cells              |
+| [EMDB](https://www.ebi.ac.uk/emdb/)                                                  | Protein, Viruses   |
 | [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     |

extension/__init__.py

@@ -9,6 +9,8 @@ auto_load.init()
 
 def register():
     auto_load.register()
+    bpy.types.WindowManager.bioxelnodes_progress_factor = bpy.props.FloatProperty()
+    bpy.types.WindowManager.bioxelnodes_progress_text = bpy.props.StringProperty()
     menus.add()
 
 

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 = "0.2.7"
+version = "0.2.9"
 name = "Bioxel Nodes"
 tagline = "For scientific volumetric data visualization in Blender"
 maintainer = "Ma Nan <icrdr2010@outlook.com>"
@@ -15,7 +15,7 @@ website = "https://omoolab.github.io/BioxelNodes/latest"
 
 # Optional list defined by Blender and server, see:
 # https://docs.blender.org/manual/en/dev/advanced/extensions/tags.html
-tags = ["Geometry Nodes", "Render"]
+tags = ["Geometry Nodes", "Render", "Import-Export"]
 
 blender_version_min = "4.2.0"
 # Optional: maximum supported Blender version
@@ -38,7 +38,11 @@ platforms = ["windows-x64"]
 # Optional: bundle 3rd party Python modules.
 # https://docs.blender.org/manual/en/dev/advanced/extensions/python_wheels.html
 wheels = [
-  "./wheels/SimpleITK-2.3.1-cp311-cp311-win_amd64.whl"
+  "./wheels/SimpleITK-2.3.1-cp311-cp311-win_amd64.whl",
+  "./wheels/lxml-5.2.2-cp311-cp311-win_amd64.whl",
+  "./wheels/tifffile-2024.7.21-py3-none-any.whl",
+  "./wheels/pyometiff-1.0.0-py3-none-any.whl",
+  "./wheels/mrcfile-1.5.1-py2.py3-none-any.whl"
 ]
 
 

mkdocs.yml

@@ -13,7 +13,7 @@ nav:
       - Prepare Your Data: prepare_data.md
       - Step by Step: step_by_step.md
       - Concepts & Pipeline: concept.md
-  - Visualizating any Bio-structure:
+  - Visualizing any Bio-structure:
       - Import & Preprocess: import.md
       - Mask Methods: mask.md
       - Assgin a Shader: shader.md

poetry.lock

@@ -539,6 +539,49 @@ files = [
     {file = "idna-3.7.tar.gz", hash = "sha256:028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc"},
 ]
 
+[[package]]
+name = "imagecodecs"
+version = "2024.6.1"
+description = "Image transformation, compression, and decompression codecs"
+optional = false
+python-versions = ">=3.9"
+files = [
+    {file = "imagecodecs-2024.6.1-cp310-cp310-macosx_10_14_x86_64.whl", hash = "sha256:369816eaddfe6e9d8d1faa6794341c89f3494fef846c9b5d834f77dc7583bfdf"},
+    {file = "imagecodecs-2024.6.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:9300198b5e4ec09f94f5d6bdd6f727d02bbccba5ed0c974e9931d3f9d5d7fa35"},
+    {file = "imagecodecs-2024.6.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:42eafc88b3dd44cfb7a8b076ff64ff794874e88d45c3691b32e9e93fbc42e86e"},
+    {file = "imagecodecs-2024.6.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:f428f141ed102cecf98ffbe61ed02b1f3f7d65db0bf1459cf2e7b1a53fb279b2"},
+    {file = "imagecodecs-2024.6.1-cp310-cp310-win32.whl", hash = "sha256:5526a7e41939613a5c68403911f7cc738f6fe1a8ac0456535720f53253497b76"},
+    {file = "imagecodecs-2024.6.1-cp310-cp310-win_amd64.whl", hash = "sha256:8d3d82ebe83a3e31ab7f09a8b72155c5436a3f87145052ca57dc5caf3a2dc9c0"},
+    {file = "imagecodecs-2024.6.1-cp311-cp311-macosx_10_14_x86_64.whl", hash = "sha256:328ea133e0f292cf54c5feb13e247fbf45a6055c8dc6822e841c208d2dc5c96a"},
+    {file = "imagecodecs-2024.6.1-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:8045ea3a9c9de78ea00e2a387f47d784434bfad05967decbe0c1b3bee5aadf25"},
+    {file = "imagecodecs-2024.6.1-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:42bd9ec14e4d38f15e2fa387c90b726dba42c16da0a9b6ff2c23e01478b8cd93"},
+    {file = "imagecodecs-2024.6.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:9eb5b2d755a64de9a7e0604d5dcc1151c96b43b4e5ac69bebc6d8d790b77ca58"},
+    {file = "imagecodecs-2024.6.1-cp311-cp311-win32.whl", hash = "sha256:03ace438a843e024239cddbe7fe6940bd2a6cf3316b08c281b95842b5217c0f7"},
+    {file = "imagecodecs-2024.6.1-cp311-cp311-win_amd64.whl", hash = "sha256:cd926589c6e3c564490b93258b1a2ca3b040da10c21e99b618b7be6dd76b2a25"},
+    {file = "imagecodecs-2024.6.1-cp311-cp311-win_arm64.whl", hash = "sha256:101fcef57aedb8730d1d2d1779dfbaa23daf7e50cd4130e88945a4fe34d0212f"},
+    {file = "imagecodecs-2024.6.1-cp312-cp312-macosx_10_14_x86_64.whl", hash = "sha256:3c5e0ebdf7e1f8ec23a6d3c4b06fc7a64f41ec47ba23516458c5a763685f29e3"},
+    {file = "imagecodecs-2024.6.1-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:407d2859d62ed5834e69e74d9ebcbc2d30be71e4f1ee14fae37f1179110fec8c"},
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+    {file = "imagecodecs-2024.6.1-cp312-cp312-win_arm64.whl", hash = "sha256:0bd70e34ff9b14ea299c1cdc51db4a80c2c406ae2f422e5e400716e8df791bdc"},
+    {file = "imagecodecs-2024.6.1-cp39-cp39-macosx_10_14_x86_64.whl", hash = "sha256:3d39699ddf13d8ce67b6a1a04e92a9c318613c0eecc245861590fed78f09e2a1"},
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+    {file = "imagecodecs-2024.6.1-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:ababc300ec18c28e8fd515ad92252679742c243e88cdb7c5e217c72eaed8fa3a"},
+    {file = "imagecodecs-2024.6.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:fc50b613738a3b62aa77c00d457a9e9a6337e9fb7a2b8163d99a368d4a346f8d"},
+    {file = "imagecodecs-2024.6.1-cp39-cp39-win32.whl", hash = "sha256:38c6a929ca5356ab9ffdd4aa6dcae5156a7265f886b662bd8cfb0bca1e3d6bee"},
+    {file = "imagecodecs-2024.6.1-cp39-cp39-win_amd64.whl", hash = "sha256:01e41f59ebb7b09dc965cafd264cab0ee303d3cef981ecceb85bb556b933a8f3"},
+    {file = "imagecodecs-2024.6.1-pp310-pypy310_pp73-win_amd64.whl", hash = "sha256:20d66ea962e9e6ea690a89f56ff9da7831378990d705c1fb133cddac2f2c507a"},
+    {file = "imagecodecs-2024.6.1.tar.gz", hash = "sha256:0f3e94b7f51e2f78287b7ffae82cd850b1007639148894538274fa50bd179886"},
+]
+
+[package.dependencies]
+numpy = "*"
+
+[package.extras]
+all = ["matplotlib", "numcodecs", "tifffile"]
+
 [[package]]
 name = "imageio"
 version = "2.34.2"
@@ -784,6 +827,164 @@ dev = ["changelist (==0.5)"]
 lint = ["pre-commit (==3.7.0)"]
 test = ["pytest (>=7.4)", "pytest-cov (>=4.1)"]
 
+[[package]]
+name = "lxml"
+version = "5.2.2"
+description = "Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API."
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "lxml-5.2.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:364d03207f3e603922d0d3932ef363d55bbf48e3647395765f9bfcbdf6d23632"},
+    {file = "lxml-5.2.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:50127c186f191b8917ea2fb8b206fbebe87fd414a6084d15568c27d0a21d60db"},
+    {file = "lxml-5.2.2-cp310-cp310-manylinux_2_12_i686.manylinux2010_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:74e4f025ef3db1c6da4460dd27c118d8cd136d0391da4e387a15e48e5c975147"},
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+    {file = "lxml-5.2.2.tar.gz", hash = "sha256:bb2dc4898180bea79863d5487e5f9c7c34297414bad54bcd0f0852aee9cfdb87"},
+]
+
+[package.extras]
+cssselect = ["cssselect (>=0.7)"]
+html-clean = ["lxml-html-clean"]
+html5 = ["html5lib"]
+htmlsoup = ["BeautifulSoup4"]
+source = ["Cython (>=3.0.10)"]
+
 [[package]]
 name = "markdown"
 version = "3.6"
@@ -1075,6 +1276,20 @@ files = [
 griffe = ">=0.37"
 mkdocstrings = ">=0.20"
 
+[[package]]
+name = "mrcfile"
+version = "1.5.1"
+description = "MRC file I/O library"
+optional = false
+python-versions = "*"
+files = [
+    {file = "mrcfile-1.5.1-py2.py3-none-any.whl", hash = "sha256:06900f1245e66dd4617cbd4a7117a2d75d53fc4e5b74d811766f71a858b059a9"},
+    {file = "mrcfile-1.5.1.tar.gz", hash = "sha256:403c4bb0ac842410ce5ea501f4fddc91ea37c12ef869d508d3ac571868d82ac2"},
+]
+
+[package.dependencies]
+numpy = ">=1.16.0"
+
 [[package]]
 name = "nest-asyncio"
 version = "1.6.0"
@@ -1396,13 +1611,13 @@ tests = ["pytest"]
 
 [[package]]
 name = "pycodestyle"
-version = "2.11.1"
+version = "2.12.0"
 description = "Python style guide checker"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "pycodestyle-2.11.1-py2.py3-none-any.whl", hash = "sha256:44fe31000b2d866f2e41841b18528a505fbd7fef9017b04eff4e2648a0fadc67"},
-    {file = "pycodestyle-2.11.1.tar.gz", hash = "sha256:41ba0e7afc9752dfb53ced5489e89f8186be00e599e712660695b7a75ff2663f"},
+    {file = "pycodestyle-2.12.0-py2.py3-none-any.whl", hash = "sha256:949a39f6b86c3e1515ba1787c2022131d165a8ad271b11370a8819aa070269e4"},
+    {file = "pycodestyle-2.12.0.tar.gz", hash = "sha256:442f950141b4f43df752dd303511ffded3a04c2b6fb7f65980574f0c31e6e79c"},
 ]
 
 [[package]]
@@ -1448,6 +1663,26 @@ pyyaml = "*"
 [package.extras]
 extra = ["pygments (>=2.12)"]
 
+[[package]]
+name = "pyometiff"
+version = "1.0.0"
+description = "Read and Write OME-TIFFs in Python"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "pyometiff-1.0.0-py3-none-any.whl", hash = "sha256:6c274786f32b9bd662105af37419c7f2f7ee6194bc1a7283b4ab2a00c53cf632"},
+    {file = "pyometiff-1.0.0.tar.gz", hash = "sha256:596b7a7377a5f2e50292aa52dd22e6347a2d2f21577e93d1fcdcd63942e597f7"},
+]
+
+[package.dependencies]
+imagecodecs = "*"
+lxml = "*"
+numpy = "*"
+tifffile = ">2020.10.1"
+
+[package.extras]
+dev = ["mock", "pytest (>3.7)"]
+
 [[package]]
 name = "pyparsing"
 version = "3.1.2"
@@ -2225,4 +2460,4 @@ cffi = ["cffi (>=1.11)"]
 [metadata]
 lock-version = "2.0"
 python-versions = "~=3.10.0"
-content-hash = "e9980867106af8e9e7524ff319d3c0785906b359022595732260fd4b3ca135ca"
+content-hash = "5eb6cfca92f09b1f4bba15042adc44cafa174f28d7b4520bde92f0f7235fd233"

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "bioxelnodes"
-version = "0.2.7"
+version = "0.2.9"
 description = ""
 authors = ["Ma Nan <icrdr2010@outlook.com>"]
 license = "MIT"
@@ -11,6 +11,8 @@ python = "~=3.10.0"
 bpy = "~=4.0"
 simpleitk = "^2.3.1"
 scikit-image = "^0.24.0"
+pyometiff = "^1.0.0"
+mrcfile = "^1.5.1"
 
 [tool.poetry.group.dev.dependencies]
 ipykernel = "^6.25.2"