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Merge pull request #31 from OmooLab/feature/dev

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Feature/dev
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Ma Nan
2024-07-23 12:05:18 +08:00
committed by GitHub
parent 50e8564027 c9a961d5e8
commit 9b36e9d911
5 changed files with 169 additions and 103 deletions
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26
README.md
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@@ -2,23 +2,27 @@
# 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)
![Static Badge](https://img.shields.io/badge/Blender-orange?style=for-the-badge&logo=blender&logoColor=white&color=black)
![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&link=https%3A%2F%2Fdiscord.gg%2FpYkNyq2TjE)
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
@@ -55,7 +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**

25
bioxelnodes/io.py
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@@ -175,6 +175,9 @@ class ParseVolumetricData(bpy.types.Operator):
progress_callback=progress_callback)
except CancelledByUser:
return
except RuntimeError:
self.has_error = True
return
if cancel():
return
@@ -183,6 +186,8 @@ class ParseVolumetricData(bpy.types.Operator):
# Init cancel flag
self.is_cancelled = False
self.has_error = False
# Create the thread
self.thread = threading.Thread(target=parse_volumetric_data_func,
args=(self, context, lambda: self.is_cancelled))
@@ -229,6 +234,11 @@ class ParseVolumetricData(bpy.types.Operator):
self.report({"WARNING"}, "Canncelled by user.")
return {'CANCELLED'}
# Check if thread is cancelled by user
if self.has_error:
self.report({"ERROR"}, "Fail to parse, something went wrong.")
return {'CANCELLED'}
# If not canncelled...
for key, value in self.meta.items():
print(f"{key}: {value}")
@@ -239,9 +249,12 @@ class ParseVolumetricData(bpy.types.Operator):
orig_spacing[1], orig_spacing[2])
bioxel_size = max(min_size, 1.0)
layer_size = get_layer_size(orig_shape,
layer_shape = get_layer_shape(1, orig_shape, orig_spacing)
layer_size = get_layer_size(layer_shape,
bioxel_size)
log10 = math.floor(math.log10(max(*layer_size)))
log10 = max(1,log10)
log10 = min(3,log10)
scene_scale = math.pow(10, -log10)
if self.container:
@@ -700,6 +713,7 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
container.matrix_world = mat_ras2blender @ mat_scene_scale
container.name = container_name
container.show_in_front = True
container.data.name = container_name
container['bioxel_container'] = True
@@ -741,8 +755,8 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
layer.hide_select = True
layer.hide_render = True
layer.hide_viewport = True
layer.data.display.use_slice = True
layer.data.display.density = 1e-05
# layer.data.display.use_slice = True
# layer.data.display.density = 1e-05
layer['bioxel_layer'] = True
layer['bioxel_layer_type'] = layer_info['type']
@@ -811,11 +825,8 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
# Change render setting for better result
preferences = context.preferences.addons[__package__].preferences
if preferences.do_change_render_setting and self.is_first_import:
if bpy.app.version < (4, 2, 0):
bpy.context.scene.render.engine = 'CYCLES'
bpy.context.scene.render.engine = 'CYCLES'
try:
bpy.context.scene.cycles.shading_system = True
bpy.context.scene.cycles.volume_bounces = 12

4
bioxelnodes/operators.py
View File

@@ -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']

183
bioxelnodes/parse.py
View File

@@ -11,6 +11,9 @@ try:
except:
...
"""
Convert any volumetric data to 3D numpy array with order TXYZC
"""
SUPPORT_EXTS = ['', '.dcm', '.DCM', '.DICOM', '.ima', '.IMA',
'.bmp', '.BMP',
@@ -40,7 +43,7 @@ SEQUENCE_EXTS = ['.bmp', '.BMP',
'.tif', '.TIF', '.tiff', '.TIFF',
'.png', '.PNG']
DICOM_EXTS = ['', '.dcm', '.DCM', '.DICOM']
DICOM_EXTS = ['', '.dcm', '.DCM', '.DICOM', '.ima', '.IMA']
FH_EXTS = ['', '.dcm', '.DCM', '.DICOM', '.ima', '.IMA',
'.gipl', '.gipl.gz',
@@ -136,7 +139,11 @@ def parse_volumetric_data(filepath: str, series_id="", progress_callback=None):
if len(sequence) > 1:
is_sequence = True
if ext in MRC_EXTS and not is_sequence:
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
@@ -159,10 +166,10 @@ def parse_volumetric_data(filepath: str, series_id="", progress_callback=None):
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": "",
@@ -175,7 +182,9 @@ def parse_volumetric_data(filepath: str, series_id="", progress_callback=None):
"is_oriented": False
}
elif ext in OME_EXTS and not is_sequence:
# 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()
@@ -189,69 +198,70 @@ def parse_volumetric_data(filepath: str, series_id="", progress_callback=None):
# 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:
ome_order = "TCZYX"
...
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
}
else:
# 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()
@@ -294,10 +304,13 @@ def parse_volumetric_data(filepath: str, series_id="", progress_callback=None):
name = name.replace(" ", "-")
description = description.replace(" ", "-")
elif ext in SEQUENCE_EXTS:
itk_volume = sitk.ReadImage(sequence)
name = get_sequence_name(filepath).replace(" ", "-")
description = ""
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(" ", "-")
@@ -311,7 +324,33 @@ def parse_volumetric_data(filepath: str, series_id="", progress_callback=None):
if not progressing:
raise CancelledByUser
if itk_volume.GetDimension() == 3:
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)
@@ -332,12 +371,12 @@ def parse_volumetric_data(filepath: str, series_id="", progress_callback=None):
"spacing": tuple(itk_volume.GetSpacing()),
"origin": tuple(itk_volume.GetOrigin()),
"direction": tuple(itk_volume.GetDirection()),
"frame_count": volume.shape[0],
"frame_count": 1,
"channel_count": volume.shape[-1],
"is_oriented": True
}
if itk_volume.GetDimension() == 4:
elif itk_volume.GetDimension() == 4:
# FIXME: not sure...
direction = np.array(itk_volume.GetDirection())
direction = direction.reshape(3, 3) if itk_volume.GetDimension() == 3 \

34
docs/index.md
View File

@@ -1,17 +1,28 @@
[中文文档](https://uj6xfhbzp0.feishu.cn/wiki/Qx3VwHuNPimeI8kr6nDcvl1DnHf?from=from_copylink)
# Bioxel Nodes
![Static Badge](https://img.shields.io/badge/Blender-orange?style=for-the-badge&logo=blender&logoColor=white&color=black)
![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&link=https%3A%2F%2Fdiscord.gg%2FpYkNyq2TjE)
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
@@ -48,7 +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**
@@ -59,6 +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
- Better multi-format import experience
- One-click bake model with texture
- AI Segmentation to Generate Labels