feat: more time sequence choice

fix: contrast formulation cause leak of high value
fix: empty series_id cause fail to read
chore: restructure folder
chore!: change layer vars
BREAKING CHANGE: not support 4.1 any more

.github/workflows/upload-assets.yml → .github/workflows/build-addon.yml

@@ -50,33 +50,13 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
-  upload_blender_addon:
-    name: Upload Blender Add-on
-    needs: draft_release
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout Code
-        uses: actions/checkout@v4
-        with:
-          lfs: "true"
-      - name: Zip Add-on
-        run: |
-          zip -r package.zip bioxelnodes
-      - name: Upload Release Asset
-        id: upload-release-asset
-        uses: actions/upload-release-asset@v1
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        with:
-          upload_url: ${{ needs.draft_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps
-          asset_path: ./package.zip
-          asset_name: BioxelNodes_Addon_${{ needs.draft_release.outputs.version }}.zip
-          asset_content_type: application/zip
-
-  upload_blender_extension:
-    name: Upload Blender Extension
+  build_blender_add-on:
+    name: Build Blender Extension
     needs: draft_release
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        platform: ["windows-x64", "linux-x64", "macos-arm64", "macos-x64"]
     steps:
       - name: Checkout Code
         uses: actions/checkout@v4
@@ -86,21 +66,10 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: 3.11
-      - name: Zip Extension
+      - name: Build Add-on
         run: |
-          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
-          cp extension/blender_manifest.toml bioxelnodes/blender_manifest.toml
+          pip install tomlkit
+          python build.py ${{ matrix.platform }}
           zip -r package.zip bioxelnodes
       - name: Upload Release Asset
         id: upload-release-asset
@@ -110,5 +79,5 @@ jobs:
         with:
           upload_url: ${{ needs.draft_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps
           asset_path: ./package.zip
-          asset_name: BioxelNodes_Extension_${{ needs.draft_release.outputs.version }}.zip
+          asset_name: BioxelNodes_${{ needs.draft_release.outputs.version }}_${{ matrix.platform }}.zip
           asset_content_type: application/zip

.gitignore

@@ -133,4 +133,4 @@ blendcache_*
 
 .secrets
 
-!bioxelnodes/scipy/_nd_image.cp311-win_amd64.pyd
+!scipy_ndimage/*/**

README.md

@@ -13,7 +13,7 @@ Bioxel Nodes is a Blender addon for scientific volumetric data visualization. It
 
 ![cover](https://omoolab.github.io/BioxelNodes/latest/assets/cover.png)
 
--   Fantastic rendering result, also support EEVEE NEXT.
+-   Realistic rendering result, also support EEVEE NEXT.
 -   Support multiple formats.
 -   Support 4D volumetric data.
 -   All kinds of cutters.
@@ -61,13 +61,13 @@ Welcome to our [discord server](https://discord.gg/pYkNyq2TjE), if you have any
 
 ## Compatible to Newer Version
 
-**Updating this addon may break old files, so read the following carefully before updating**
+**v0.3.x is not compatible to v0.2.x, Updating this addon may break old files. Read the following carefully before upgradation**
 
-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.
+Before upgradation, 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.
+Also, 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
 

bioxelnodes/__init__.py

@@ -4,17 +4,6 @@
 from . import menus
 
 
-bl_info = {
-    "name": "Bioxel Nodes",
-    "author": "Ma Nan",
-    "description": "",
-    "blender": (4, 1, 0),
-    "version": (0, 2, 9),
-    "location": "File -> Import",
-    "warning": "",
-    "category": "Node"
-}
-
 auto_load.init()
 
 

bioxelnodes/bioxel/container.py

@@ -0,0 +1,9 @@
+from .layer import Layer
+
+
+class Container():
+    def __init__(self,
+                 name,
+                 layers: list[Layer] = []) -> None:
+        self.name = name
+        self.layers = layers

bioxelnodes/bioxel/io.py

@@ -0,0 +1,43 @@
+from pathlib import Path
+import uuid
+
+
+# 3rd-party
+import h5py
+
+from .container import Container
+from .layer import Layer
+
+
+def load_container(load_file: str):
+    load_path = Path(load_file).resolve()
+    with h5py.File(load_path, 'r') as file:
+        layers = []
+        for key, layer_dset in file['layers'].items():
+            layers.append(Layer(data=layer_dset[:],
+                                name=layer_dset.attrs['name'],
+                                kind=layer_dset.attrs['kind'],
+                                affine=layer_dset.attrs['affine']))
+
+        container = Container(name=file.attrs['name'],
+                              layers=layers)
+
+        return container
+
+
+def save_container(container: Container, save_file: str, overwrite=False):
+    save_path = Path(save_file).resolve()
+    if overwrite:
+        if save_path.is_file():
+            save_path.unlink()
+
+    with h5py.File(save_path, "w") as file:
+        file.attrs['name'] = container.name
+        layer_group = file.create_group("layers")
+        for layer in container.layers:
+            layer_key = uuid.uuid4().hex[:8]
+            layer_dset = layer_group.create_dataset(name=layer_key,
+                                                    data=layer.data)
+            layer_dset.attrs['name'] = layer.name
+            layer_dset.attrs['kind'] = layer.kind
+            layer_dset.attrs['affine'] = layer.affine

bioxelnodes/bioxel/layer.py

@@ -0,0 +1,131 @@
+import copy
+import numpy as np
+
+from . import scipy
+from . import skimage as ski
+
+# 3rd-party
+import transforms3d
+
+# TODO: turn to dataclasses
+
+
+class Layer():
+    def __init__(self,
+                 data: np.ndarray,
+                 name: str,
+                 kind="scalar",
+                 affine=np.identity(4)) -> None:
+        if data.ndim != 5:
+            raise Exception("Data shape order should be TXYZC")
+
+        affine = np.array(affine)
+        if affine.shape != (4, 4):
+            raise Exception("affine shape should be (4,4)")
+
+        self.data = data
+        self.name = name
+        self.kind = kind
+        self.affine = affine
+
+    @property
+    def bioxel_size(self):
+        t, r, z, s = transforms3d.affines.decompose44(self.affine)
+        return z.tolist()
+
+    @property
+    def shape(self):
+        return self.data.shape[1:4]
+
+    @property
+    def dtype(self):
+        return self.data.dtype
+
+    @property
+    def origin(self):
+        t, r, z, s = transforms3d.affines.decompose44(self.affine)
+        return t.tolist()
+
+    @property
+    def euler(self):
+        t, r, z, s = transforms3d.affines.decompose44(self.affine)
+        return list(transforms3d.euler.mat2euler(r))
+
+    @property
+    def min(self):
+        return float(np.min(self.data))
+
+    @property
+    def frame_count(self):
+        return self.data.shape[0]
+
+    @property
+    def channel_count(self):
+        return self.data.shape[-1]
+
+    @property
+    def max(self):
+        return float(np.max(self.data))
+
+    def copy(self):
+        return copy.deepcopy(self)
+
+    def fill(self, value: float, mask: np.ndarray):
+        mask_frames = ()
+        if mask.ndim == 4:
+            if mask.shape[0] != self.frame_count:
+                raise Exception("Mask frame count is not same as ")
+            for f in range(self.frame_count):
+                mask_frame = mask[f, :, :, :]
+                mask_frame = scipy.median_filter(
+                    mask_frame.astype(np.float32), size=2)
+                mask_frames += (mask_frame,)
+        elif mask.ndim == 3:
+            for f in range(self.frame_count):
+                mask_frame = mask[:, :, :]
+                mask_frame = scipy.median_filter(
+                    mask_frame.astype(np.float32), size=2)
+                mask_frames += (mask_frame,)
+        else:
+            raise Exception("Mask shape order should be TXYZ or XYZ")
+
+        _mask = np.stack(mask_frames)
+        _mask = np.expand_dims(_mask, axis=-1)
+        self.data = _mask * value + (1-_mask) * self.data
+
+    def resize(self, shape:tuple, progress_callback=None):
+        if len(shape) != 3:
+            raise Exception("Shape must be 3 dim")
+
+        data = self.data
+
+        # TXYZC > TXYZ
+        if self.kind in ['label', 'scalar']:
+            data = np.amax(data, -1)
+
+        if self.kind in ['scalar']:
+            dtype = data.dtype
+            data = data.astype(np.float32)
+
+        data_frames = ()
+        for f in range(self.frame_count):
+            if progress_callback:
+                progress_callback(f, self.frame_count)
+
+            frame = ski.resize(data[f, :, :, :],
+                               shape,
+                               preserve_range=True,
+                               anti_aliasing=data.dtype.kind != "b")
+
+            data_frames += (frame,)
+
+        data = np.stack(data_frames)
+
+        if self.kind in ['scalar']:
+            data = data.astype(dtype)
+
+        # TXYZ > TXYZC
+        if self.kind in ['label', 'scalar']:
+            data = np.expand_dims(data, axis=-1)  # expend channel
+
+        self.data = data