WIP: improve vcml image based geometry handling

Author: jcschaff

pyvcell/vcml/models.py

@@ -150,14 +150,16 @@ class PixelClass(VcmlNode):
 class Image(VcmlNode):
     name: str
     size: tuple[int, int, int]
-    compressed_size: int
+    uncompressed_size: int
     compressed_content: str
     pixel_classes: list[PixelClass] = Field(default_factory=list)
 
     @property
     def ndarray_3d_u8(self) -> NDArray3Du8:
         compressed_bytes = bytes.fromhex(self.compressed_content)
         raw_pixels = zlib.decompress(compressed_bytes)
+        if len(raw_pixels) != self.uncompressed_size:
+            raise ValueError("Decompressed size does not match compressed size")
         return np.frombuffer(raw_pixels, dtype=np.uint8).astype(np.uint8).reshape(self.size)
 
     @staticmethod
@@ -175,7 +177,7 @@ def from_ndarray_3d_u8(ndarray_3d_u8: NDArray3Du8, name: str) -> "Image":
         return Image(
             name=name,
             size=size,
-            compressed_size=len(raw_pixels),
+            uncompressed_size=len(raw_pixels),
             compressed_content=compressed_bytes.hex(),
             pixel_classes=pixel_classes,
         )

pyvcell/vcml/vcml_geo_from_images.py

@@ -51,9 +51,3 @@ def read_images_to_volume(image_path: Path) -> NDArray3Du8:
     vcell_image: vc.Image = vc.Image.from_ndarray_3d_u8(ndarray_3d_u8=orig_image_array, name="bunny")
     vcell_image_array = vcell_image.ndarray_3d_u8
     print(vcell_image.pixel_classes)
-
-    # using matplotlib, plot the middle image in the volume
-    import matplotlib.pyplot as plt
-
-    plt.imshow(np.transpose(vcell_image_array, (1, 0, 2))[40])
-    plt.show()

pyvcell/vcml/vcml_reader.py

@@ -237,7 +237,7 @@ def visit_Image(self, element: _Element, node: vc.Geometry) -> None:
         image = vc.Image(
             name=image_name,
             size=image_size,
-            compressed_size=compressed_size,
+            uncompressed_size=compressed_size,
             compressed_content=compressed_content,
             pixel_classes=pixel_classes,
         )

pyvcell/vcml/vcml_writer.py

@@ -225,7 +225,7 @@ def write_geometry(self, geometry: vc.Geometry, parent: _Element) -> None:
                 X=str(image.size[0]),
                 Y=str(image.size[1]),
                 Z=str(image.size[2]),
-                CompressedSize=str(image.compressed_size),
+                CompressedSize=str(image.uncompressed_size),
             )
             image_data_element.text = image.compressed_content
             image_element.append(image_data_element)