Merge pull request #38 from OmooLab/fix-import

fix: color ramp not fit

bioxelnodes/bioxel/layer.py

@@ -3,6 +3,7 @@ import numpy as np
 
 from . import scipy
 from . import skimage as ski
+from . import scipy as ndi
 
 # 3rd-party
 import transforms3d
@@ -97,36 +98,43 @@ class Layer():
         _mask = np.expand_dims(_mask, axis=-1)
         self.data = _mask * value + (1-_mask) * self.data
 
-    def resize(self, shape:tuple, progress_callback=None):
+    def resize(self, shape: tuple, progress_callback=None):
         if len(shape) != 3:
             raise Exception("Shape must be 3 dim")
 
         data = self.data
+        order = 0 if self.dtype == bool else 1
 
         # TXYZC > TXYZ
         if self.kind in ['label', 'scalar']:
             data = np.amax(data, -1)
 
-        if self.kind in ['scalar']:
+        # if self.kind in ['scalar']:
-            dtype = data.dtype
+        #     dtype = data.dtype
-            data = data.astype(np.float32)
+            # 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, :, :, :],
+            # frame = ski.resize(data[f, :, :, :],
-                               shape,
+            #                    shape,
-                               preserve_range=True,
+            #                    preserve_range=True,
-                               anti_aliasing=data.dtype.kind != "b")
+            #                    anti_aliasing=data.dtype.kind != "b")
+
+            factors = np.divide(self.shape, shape)
+            zoom_factors = [1 / f for f in factors]
+            frame = ndi.zoom(data[f, :, :, :],
+                             zoom_factors,
+                             order=order)
 
             data_frames += (frame,)
 
         data = np.stack(data_frames)
 
-        if self.kind in ['scalar']:
+        # if self.kind in ['scalar']:
-            data = data.astype(dtype)
+        #     data = data.astype(dtype)
 
         # TXYZ > TXYZC
         if self.kind in ['label', 'scalar']:

bioxelnodes/blender_manifest.toml

@@ -1,7 +1,7 @@
 schema_version = "1.0.0"
 
 id = "bioxelnodes"
-version = "0.3.2"
+version = "0.3.3"
 name = "Bioxel Nodes"
 tagline = "For scientific volumetric data visualization in Blender"
 maintainer = "Ma Nan <icrdr2010@outlook.com>"

bioxelnodes/operators/io.py

@@ -134,10 +134,12 @@ class ParseVolumetricData(bpy.types.Operator):
     filepath: bpy.props.StringProperty(subtype="FILE_PATH")  # type: ignore
 
     skip_read_as: bpy.props.BoolProperty(name="Skip Read As",
-                                         default=False)  # type: ignore
+                                         default=False,
+                                         options={"SKIP_SAVE"})  # type: ignore
 
     skip_series_select: bpy.props.BoolProperty(name="Skip Sries Select",
-                                               default=True)  # type: ignore
+                                               default=True,
+                                               options={"SKIP_SAVE"})  # type: ignore
 
     read_as: bpy.props.EnumProperty(name="Read as",
                                     default="scalar",

bioxelnodes/operators/layer.py

@@ -232,7 +232,6 @@ class CombineLabels(bpy.types.Operator, LabelOperator):
             return {'FINISHED'}
         base_obj = label_objs[0]
         label_objs = label_objs[1:]
-        container_obj = base_obj.parent
 
         base_layer = obj_to_layer(base_obj)
         modified_layer = base_layer.copy()
@@ -241,7 +240,7 @@ class CombineLabels(bpy.types.Operator, LabelOperator):
         for label_obj in label_objs:
             label_layer = obj_to_layer(label_obj)
             label_layer.resize(base_layer.shape)
-            modified_layer.data = np.maximum(base_layer.data, label_layer.data)
+            modified_layer.data = np.maximum(modified_layer.data, label_layer.data)
             label_names.append(label_layer.name)
 
         modified_layer.name = f"{'-'.join(label_names)}-Combined"

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "bioxelnodes"
-version = "0.3.2"
+version = "0.3.3"
 description = ""
 authors = ["Ma Nan <icrdr2010@outlook.com>"]
 license = "MIT"