- allow None in Transform.from_dict

- None transform parameters -> unit parameters/matrix

ndbioimage/__init__.py

@@ -24,8 +24,8 @@ from pint import set_application_registry
 from tiffwrite import FrameInfo, IJTiffParallel
 from tqdm.auto import tqdm
 
-from .jvm import JVM, JVMException
-from .transforms import Transform, Transforms
+from .jvm import JVM, JVMException  # noqa: F401
+from .transforms import Transform, Transforms  # noqa: F401
 
 try:
     __version__ = version(Path(__file__).parent.name)
@@ -596,12 +596,12 @@ class Imread(np.lib.mixins.NDArrayOperatorsMixin, ABC):
             elif self.path.with_suffix('.pzl').exists():
                 pname = self.path.with_suffix('.pzl')
             else:
-                return
+                return None
             try:
                 return self.get_config(pname)
             except Exception:  # noqa
-                return
-        return
+                return None
+        return None
 
     @property
     def ndim(self) -> int:

ndbioimage/transforms.py

@@ -321,11 +321,12 @@ class Transform:
     @classmethod
     def from_dict(cls, d):
         new = cls()
-        new.origin = [None if i is None else float(i) for i in d['CenterOfRotationPoint']]
-        new.parameters = [None if i is None else float(i) for i in d['TransformParameters']]
-        new.dparameters = ([None if i is None else float(i) for i in d['dTransformParameters']]
-                           if 'dTransformParameters' in d else 6 * [np.nan])
-        new.shape = [None if i is None else float(i) for i in d['Size']]
+        new.origin = None if d['CenterOfRotationPoint'] is None else [float(i) for i in d['CenterOfRotationPoint']]
+        new.parameters = ((1., 0., 0., 1., 0., 0.) if d['TransformParameters'] is None else
+                          [float(i) for i in d['TransformParameters']])
+        new.dparameters = ([(0., 0., 0., 0., 0., 0.) if i is None else float(i) for i in d['dTransformParameters']]
+                           if 'dTransformParameters' in d else 6 * [np.nan] and d['dTransformParameters'] is not None)
+        new.shape = None if d['Size'] is None else [None if i is None else float(i) for i in d['Size']]
         return new
 
     def __mul__(self, other):  # TODO: take care of dmatrix
@@ -382,6 +383,8 @@ class Transform:
     def parameters(self):
         if self.transform is not None:
             return list(self.transform.GetParameters())
+        else:
+            return [1., 0., 0., 1., 0., 0.]
 
     @parameters.setter
     def parameters(self, value):

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "ndbioimage"
-version = "2025.2.0"
+version = "2025.2.1"
 description = "Bio image reading, metadata and some affine registration."
 authors = ["W. Pomp <w.pomp@nki.nl>"]
 license = "GPLv3"