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reproduction_effort/functions/ImageAlignment.py

@@ -310,12 +310,14 @@ class ImageAlignment(torch.nn.Module):
             (array.shape[0], array.shape[1] * array.shape[2])
         ).argmax(dim=1)
         pos_0 = max_pos // array.shape[2]
+
         max_pos -= pos_0 * array.shape[2]
         ret = torch.zeros(
             (array.shape[0], 2), dtype=self.default_dtype, device=self.device
         )
         ret[:, 0] = pos_0
         ret[:, 1] = max_pos
+
         return ret.type(dtype=torch.int64)
 
     def _apodize(self, what: torch.Tensor) -> torch.Tensor:
@@ -666,6 +668,7 @@ class ImageAlignment(torch.nn.Module):
         array *= mask2
 
         tvec = self._argmax_ext(array, "inf")
+
         tvec = self._interpolate(array_orig, tvec)
 
         success = self._get_success(array_orig, tvec, 2)
@@ -793,7 +796,8 @@ class ImageAlignment(torch.nn.Module):
                 / (
                     torch.abs(image_reference_fft) * torch.abs(images_todo_fft)
                     + eps.unsqueeze(-1).unsqueeze(-1)
-                )
+                ),
+                dim=(-2, -1),
             )
         )
 
@@ -813,6 +817,7 @@ class ImageAlignment(torch.nn.Module):
         ret, succ = self._phase_correlation(
             im0.unsqueeze(0), im1, self.argmax_translation
         )
+
         return ret, succ
 
     def _get_ang_scale(

reproduction_effort/functions/align_cameras.py

@@ -61,12 +61,12 @@ def align_cameras(
     # --- Calculate translation and rotation between the reference images ---
     angle_refref, tvec_refref, ref_image_acceptor, ref_image_donor = align_refref(
         ref_image_acceptor=acceptor[
-            acceptor.shape[2] // 2,
+            acceptor.shape[0] // 2,
             :,
             :,
         ],
         ref_image_donor=donor[
-            donor.shape[2] // 2,
+            donor.shape[0] // 2,
             :,
             :,
         ],
@@ -77,7 +77,7 @@ def align_cameras(
 
     ref_image_oxygenation = tv.transforms.functional.affine(
         img=oxygenation[
-            oxygenation.shape[2] // 2,
+            oxygenation.shape[0] // 2,
             :,
             :,
         ].unsqueeze(0),
@@ -102,7 +102,7 @@ def align_cameras(
     ref_image_oxygenation = ref_image_oxygenation.squeeze(0)
 
     ref_image_volume = volume[
-        volume.shape[2] // 2,
+        volume.shape[0] // 2,
         :,
         :,
     ].clone()

reproduction_effort/functions/align_refref.py

@@ -16,9 +16,9 @@ def align_refref(
 ) -> tuple[torch.Tensor, torch.Tensor, torch.Tensor, torch.Tensor]:
 
     angle_refref = calculate_rotation(
-        image_alignment,
+        image_alignment=image_alignment,
-        ref_image_acceptor.unsqueeze(0),
+        input=ref_image_acceptor.unsqueeze(0),
-        ref_image_donor,
+        reference_image=ref_image_donor,
         batch_size=batch_size,
     )
 
@@ -33,9 +33,9 @@ def align_refref(
     )
 
     tvec_refref = calculate_translation(
-        image_alignment,
+        image_alignment=image_alignment,
-        ref_image_acceptor,
+        input=ref_image_acceptor,
-        ref_image_donor,
+        reference_image=ref_image_donor,
         batch_size=batch_size,
     )
 
@@ -49,8 +49,6 @@ def align_refref(
         shear=0,
         interpolation=tv.transforms.InterpolationMode.BILINEAR,
         fill=fill_value,
-    )
+    ).squeeze(0)
-
-    ref_image_acceptor = ref_image_acceptor.squeeze(0)
 
     return angle_refref, tvec_refref, ref_image_acceptor, ref_image_donor