Fixing super pixel image axes

TheJacksonLaboratory · Jul 19, 2024 · 69f000e · 69f000e
1 parent b9f6d1b
commit 69f000e
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Showing 2 changed files with 5 additions and 11 deletions.
diff --git a/src/napari_activelearning/_acquisition.py b/src/napari_activelearning/_acquisition.py
@@ -283,15 +283,10 @@ def compute_acquisition(self, dataset_metadata, acquisition_fun,
         n_samples = 0
         img_sampling_positions = []
 
-        pred_spatial_axes = list(dataset_metadata["images"]["axes"])
-        if "C" in pred_spatial_axes:
-            pred_spatial_axes.remove("C")
-        pred_spatial_axes = "".join(pred_spatial_axes)
-
         if "masks" in dataset_metadata:
             mask_axes = dataset_metadata["masks"]["source_axes"]
         else:
-            mask_axes = pred_spatial_axes
+            mask_axes = spatial_axes
 
         pred_sel = tuple(
             slice(None) if ax in pred_spatial_axes else None
@@ -303,9 +298,9 @@ def compute_acquisition(self, dataset_metadata, acquisition_fun,
             if USING_TORCH:
                 pos = pos[0].numpy()
                 img = img[0].numpy()
-                img_sp = img_sp[0, ..., 0].numpy()
+                img_sp = img_sp.numpy().squeeze()
             else:
-                img_sp = img_sp[..., 0]
+                img_sp = img_sp.squeeze()
 
             pos = {
                 ax: slice(pos_ax[0], pos_ax[1])

diff --git a/src/napari_activelearning/_utils.py b/src/napari_activelearning/_utils.py
@@ -98,12 +98,11 @@ def _compute_transform(self, image):
 
             labels_dim = np.arange(cols * rows).reshape(rows, cols)
             labels = resize(labels_dim,
-                            (image.shape[self.axes.index("Y")],
-                             image.shape[self.axes.index("X")]),
+                            (image.shape[self.ax_Y], image.shape[self.ax_X]),
                             order=0)
 
         if image_channels > 1:
-            labels = np.expand_dims(labels, self.axes.index("C"))
+            labels = np.expand_dims(labels, self._ax_C)
         else:
             labels = labels[..., None]