fixed density importing

it seems that there is now a blender 4.1 issue where even if the underlying `.vdb` changes, if you reimport the file it still uses the preview for the 'old' version. Because of this, the created .vdb file path now contains whether or not it was centred and inverted, which makes different files and fixes the issues.
BradyAJohnston · Apr 6, 2024 · 383aa98 · 383aa98
1 parent 05ae0e1
commit 383aa98
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Showing 8 changed files with 259 additions and 236 deletions.
diff --git a/molecularnodes/io/density.py b/molecularnodes/io/density.py
@@ -40,15 +40,19 @@ def load(
     invert: bool = False,
     setup_nodes: bool = True,
     style: str = 'density_surface',
-    center: bool = False
+    center: bool = False,
+    overwrite: bool = False
 ):
-    density = parse.MRC(file_path=file_path, center=center, invert=invert)
+    density = parse.MRC(
+        file_path=file_path,
+        center=center,
+        invert=invert,
+        overwrite=overwrite
+    )
     density.create_model(
         name=name,
-        invert=invert,
         setup_nodes=setup_nodes,
-        style=style,
-        center=center
+        style=style
     )
     return density
 

diff --git a/molecularnodes/io/parse/density.py b/molecularnodes/io/parse/density.py
@@ -17,7 +17,7 @@ def __init__(self, file_path):
         self.threshold: float = None
         self.object: bpy.types.Object = None
 
-    def path_to_vdb(self, file: str):
+    def path_to_vdb(self, file: str, center: False, invert: False):
         """
         Convert a file path to a corresponding VDB file path.
 
@@ -34,6 +34,8 @@ def path_to_vdb(self, file: str):
         # Set up file paths
         folder_path = os.path.dirname(file)
         name = os.path.basename(file).split(".")[0]
+        name += "_center" if center else ""
+        name += "_invert" if invert else ""
         file_name = name + '.vdb'
         file_path = os.path.join(folder_path, file_name)
         return file_path
diff --git a/molecularnodes/io/parse/mrc.py b/molecularnodes/io/parse/mrc.py
@@ -14,21 +14,22 @@ class MRC(Density):
     that can be written as `.vdb` files and the imported into Blender as volumetric objects.
     """
 
-    def __init__(self, file_path, center=False, invert=False):
+    def __init__(self, file_path, center=False, invert=False, overwrite=False):
         super().__init__(self)
         self.file_path = file_path
         self.grid = self.map_to_grid(self.file_path, center=center)
         self.file_vdb = self.map_to_vdb(
-            self.file_path, center=center, invert=invert)
+            self.file_path,
+            center=center,
+            invert=invert,
+            overwrite=overwrite
+        )
 
     def create_model(
         self,
         name='NewDensity',
         style='density_surface',
-        setup_nodes=True,
-        invert: bool = False,
-        center: bool = False,
-        world_scale: float = 0.01
+        setup_nodes=True
     ) -> bpy.types.Object:
         """
         Loads an MRC file into Blender as a volumetric object.
@@ -39,20 +40,16 @@ def create_model(
             Path to the MRC file.
         name : str, optional
             If not None, renames the object with the new name.
-        invert : bool, optional
-            Whether to invert the data from the grid, defaulting to False. Some file types
-            such as EM tomograms have inverted values, where a high value == low density.
-        world_scale : float, optional
-            Scale of the object in the world. Defaults to 0.01.
-        center : bool, optional
-            Whether to center the volume on the origin. Defaults to False.
 
         Returns
         -------
         bpy.types.Object
             The loaded volumetric object.
         """
+        # import and ensure object is at world origin to get corect alignment with
+        # structures
         object = obj.import_vdb(self.file_vdb, collection=coll.mn())
+        object.location = (0, 0, 0)
         self.object = object
         object.mn['molecule_type'] = 'density'
 
@@ -62,7 +59,10 @@ def create_model(
 
         if setup_nodes:
             nodes.create_starting_nodes_density(
-                object, style=style, threshold=self.threshold)
+                object=object,
+                style=style,
+                threshold=self.threshold
+            )
 
         return object
 
@@ -98,7 +98,7 @@ def map_to_vdb(
         """
         import pyopenvdb as vdb
 
-        file_path = self.path_to_vdb(file)
+        file_path = self.path_to_vdb(file, center=center, invert=invert)
 
         # If the map has already been converted to a .vdb and overwrite is False, return that instead
         if os.path.exists(file_path) and not overwrite:
@@ -108,18 +108,32 @@ def map_to_vdb(
                 self.threshold = grid['MN_initial_threshold']
                 return file_path
 
+        print("Reading new file")
         # Read in the MRC file and convert it to a pyopenvdb grid
-        grid = self.map_to_grid(file, invert=invert, center=center)
+        grid = self.map_to_grid(
+            file=file,
+            invert=invert,
+            center=center
+        )
+
+        grid.transform.scale(
+            np.array((1, 1, 1)) * world_scale * grid['MN_voxel_size']
+        )
 
-        grid.transform.scale(np.array((1, 1, 1)) *
-                             world_scale * grid['MN_voxel_size'])
         if center:
-            grid.transform.translate(-np.array(grid['MN_box_size'])
-                                     * 0.5 * world_scale * grid['MN_voxel_size'])
+            offset = -np.array(grid['MN_box_size']) * 0.5
+            offset *= grid['MN_voxel_size'] * world_scale
+            print("transforming")
+            grid.transform.translate(offset)
+
+        if os.path.exists(file_path):
+            os.remove(file_path)
 
         # Write the grid to a .vdb file
+        print('writing new file')
         vdb.write(file_path, grids=[grid])
         self.threshold = grid['MN_initial_threshold']
+        del grid
 
         # Return the path to the output file
         return file_path

diff --git a/tests/snapshots/test_color/test_random_rgb/color_values.txt b/tests/snapshots/test_color/test_random_rgb/color_values.txt
@@ -1,4 +1,4 @@
-[[0.84  0.36  0.808 1.   ]
+[[0.725 0.36  0.84  1.   ]
  [0.84  0.747 0.36  1.   ]
  [0.84  0.36  0.487 1.   ]
  [0.635 0.84  0.36  1.   ]

diff --git a/...test_density/test_density_operator/False-True-False/invert_nodesetup_center_positions.txt b/...test_density/test_density_operator/False-True-False/invert_nodesetup_center_positions.txt
@@ -1,100 +1,100 @@
-[[ 1.198 -1.013  0.382]
- [-1.062  1.198  0.813]
- [ 1.004 -0.996  1.198]
- [-1.198  0.141 -0.456]
- [-0.888 -0.689  1.198]
- [ 1.198 -1.004 -0.656]
- [-0.083 -1.198 -0.025]
- [-1.198 -1.013  0.141]
- [-1.195 -1.195  0.764]
- [-1.198  1.038 -0.166]
- [ 0.365  0.456  1.198]
- [-0.614  1.198  0.282]
- [ 1.054  0.83  -1.198]
- [ 1.198 -1.096 -0.921]
- [ 0.697  1.198  0.307]
- [-0.365  0.091 -1.198]
- [-1.129 -0.515 -1.198]
- [ 1.198 -0.747 -0.573]
- [-1.198 -0.506 -0.498]
- [ 0.232 -1.198  0.697]
- [-0.739 -0.789  1.198]
- [ 1.198 -0.73   0.78 ]
- [-0.963 -1.198  0.473]
- [ 0.498  1.198  0.747]
- [ 1.198  0.091  0.008]
- [ 0.739 -1.046 -1.198]
- [ 1.198  0.639  1.179]
- [-0.133  0.647  1.198]
- [-1.145  1.198 -0.946]
- [-0.058  1.198 -0.772]
- [-1.198  0.656 -0.523]
- [-1.162 -1.198  0.888]
- [-0.349  1.198 -0.556]
- [-0.697  1.198 -0.589]
- [ 0.548  1.198 -0.838]
- [ 1.198 -0.647  0.465]
- [ 0.515  1.198  0.257]
- [ 0.05  -1.198 -0.058]
- [ 0.349  0.481  1.198]
- [ 1.198 -0.672  0.515]
- [-0.539  0.963  1.198]
- [ 0.124  1.198 -0.946]
- [-1.198  0.456 -0.647]
- [ 1.198  0.141 -0.44 ]
- [ 0.041  0.531 -1.198]
- [-0.623 -0.158 -1.198]
- [-1.198  0.664 -1.087]
- [-0.78   0.473 -1.198]
- [ 1.198 -0.755 -0.083]
- [ 0.656 -1.187 -1.198]
- [ 1.198 -0.631  0.241]
- [ 0.564 -1.198 -0.739]
- [ 0.78  -0.041 -1.198]
- [ 0.598  1.198 -0.813]
- [-1.198  0.614 -0.672]
- [ 0.805  1.087  1.198]
- [-0.946 -1.198 -0.058]
- [ 0.548  1.198 -0.158]
- [ 0.473 -0.896  1.198]
- [ 1.198 -0.872 -0.066]
- [ 0.921 -1.198  0.133]
- [-1.198  0.739 -0.73 ]
- [-1.198 -0.78   0.788]
- [-0.548  1.198  0.398]
- [ 1.071  0.598  1.198]
- [-0.855 -1.198 -0.108]
- [ 1.195 -0.971  1.195]
- [ 0.116  0.664  1.198]
- [ 1.198  0.88   1.096]
- [-0.813  0.581 -1.198]
- [-0.847 -0.797  1.198]
- [ 1.112  1.198  0.083]
- [ 1.198 -0.407  1.179]
- [ 1.198  0.581  0.938]
- [-1.096 -1.198  0.249]
- [-0.979  0.573  1.198]
- [-1.004  1.198  0.896]
- [ 0.813 -0.988  1.198]
- [ 0.531  1.198 -0.681]
- [ 1.198  0.755  0.224]
- [ 1.198 -0.639  0.664]
- [-0.232 -1.179  1.198]
- [ 1.062  1.198 -0.49 ]
- [-1.198 -0.274 -0.158]
- [ 0.423 -0.656  1.198]
- [-0.73   0.008 -1.198]
- [ 0.382 -1.198 -0.639]
- [-1.145  1.198  0.963]
- [ 0.232  0.066 -1.198]
- [ 1.038 -1.198 -0.191]
- [-0.913  0.008 -1.198]
- [-0.556  1.198  0.689]
- [-1.198  0.44   0.598]
- [-1.198  0.515 -0.813]
- [-0.365 -0.946  1.198]
- [ 1.198  0.357 -0.116]
- [ 0.93   0.481  1.198]
- [-0.581 -0.058  1.198]
- [-0.88  -1.198 -0.008]
- [-1.198  0.34   0.141]]
+[[1.195 1.529 1.23 ]
+ [0.888 0.963 1.462]
+ [1.221 1.511 0.953]
+ [1.317 0.705 0.993]
+ [0.793 0.865 1.295]
+ [0.901 0.8   0.959]
+ [1.029 0.883 1.141]
+ [1.324 1.278 1.383]
+ [1.193 1.857 1.227]
+ [1.161 1.577 0.949]
+ [1.345 1.841 1.301]
+ [1.163 0.938 1.388]
+ [1.121 0.855 1.212]
+ [1.057 0.692 1.038]
+ [1.275 0.876 0.983]
+ [1.211 1.618 1.029]
+ [1.06  1.582 1.115]
+ [1.391 1.544 1.425]
+ [1.234 1.016 1.415]
+ [1.095 1.445 1.093]
+ [1.106 1.442 1.176]
+ [1.287 1.61  1.31 ]
+ [0.967 0.743 1.1  ]
+ [1.033 1.216 1.275]
+ [1.189 1.308 1.215]
+ [1.188 1.195 1.104]
+ [1.321 2.055 1.283]
+ [1.382 1.557 1.349]
+ [1.27  0.863 0.846]
+ [1.27  1.356 1.087]
+ [1.226 1.404 1.126]
+ [1.303 1.745 1.145]
+ [0.939 0.631 1.145]
+ [1.274 0.884 1.283]
+ [1.112 0.985 1.419]
+ [0.988 0.728 1.293]
+ [1.179 0.914 1.136]
+ [1.236 1.02  1.096]
+ [1.264 0.919 0.791]
+ [1.358 1.013 1.074]
+ [1.27  2.09  1.198]
+ [0.946 0.766 1.085]
+ [1.506 1.474 1.149]
+ [1.066 1.499 1.15 ]
+ [1.383 1.067 1.09 ]
+ [1.254 1.848 1.245]
+ [1.332 0.926 1.017]
+ [0.963 0.765 1.27 ]
+ [0.833 0.838 1.259]
+ [1.185 1.964 1.177]
+ [1.116 0.595 0.868]
+ [1.278 1.261 1.262]
+ [1.171 0.853 1.486]
+ [1.22  1.565 0.917]
+ [1.009 1.216 1.456]
+ [1.361 1.502 1.061]
+ [1.178 1.542 1.195]
+ [1.241 2.087 1.166]
+ [1.3   2.005 1.099]
+ [1.272 1.561 0.97 ]
+ [1.018 0.811 0.971]
+ [1.223 1.801 1.193]
+ [1.195 0.896 1.113]
+ [1.253 0.741 0.941]
+ [1.204 1.296 1.071]
+ [1.311 0.996 1.161]
+ [1.079 0.606 1.139]
+ [1.179 0.84  1.286]
+ [1.179 2.006 1.184]
+ [0.999 1.032 1.298]
+ [0.963 0.631 1.228]
+ [1.283 1.44  1.067]
+ [1.269 1.569 1.387]
+ [1.077 1.162 1.171]
+ [1.04  1.555 1.248]
+ [0.968 0.954 1.447]
+ [1.215 1.336 1.237]
+ [1.323 1.278 1.383]
+ [1.294 0.857 0.938]
+ [1.077 0.755 1.243]
+ [1.374 1.407 1.283]
+ [1.052 1.437 1.163]
+ [1.133 1.042 1.455]
+ [1.212 1.45  1.063]
+ [1.136 0.681 0.865]
+ [1.053 0.764 1.426]
+ [1.206 1.253 1.114]
+ [1.104 0.777 0.849]
+ [1.278 2.03  1.184]
+ [1.076 1.116 1.354]
+ [0.95  0.911 0.93 ]
+ [1.055 1.137 1.137]
+ [0.932 1.177 1.155]
+ [1.048 0.647 0.913]
+ [1.331 1.071 1.326]
+ [1.099 0.984 1.286]
+ [1.145 1.253 1.159]
+ [1.275 1.472 1.148]
+ [1.224 1.547 1.299]
+ [1.237 1.573 1.158]]