Fix augmentation.

juglab · Oct 5, 2022 · 414bd5d · 414bd5d
1 parent 92d2c5f
commit 414bd5d
Showing 1 changed file with 17 additions and 11 deletions.
diff --git a/cryocare/internals/CryoCAREDataModule.py b/cryocare/internals/CryoCAREDataModule.py
@@ -17,10 +17,13 @@ def __init__(self, tomo_paths_odd=None, tomo_paths_even=None, n_samples_per_tomo
         self.n_samples_per_tomo = n_samples_per_tomo
         self.tilt_axis = tilt_axis
 
-        tilt_axis_index = ["Z", "Y", "X"].index(self.tilt_axis)
-        rot_axes = [0, 1, 2]
-        rot_axes.remove(tilt_axis_index)
-        self.rot_axes = tuple(rot_axes)
+        if self.tilt_axis is not None:
+            tilt_axis_index = ["Z", "Y", "X"].index(self.tilt_axis)
+            rot_axes = [0, 1, 2]
+            rot_axes.remove(tilt_axis_index)
+            self.rot_axes = tuple(rot_axes)
+        else:
+            self.rot_axes = None
 
         self.extraction_shapes = extraction_shapes
         self.mean = mean
@@ -60,7 +63,7 @@ def save(self, path):
 
     @classmethod
     def load(cls, path):
-        tmp = np.load(path)
+        tmp = np.load(path, allow_pickle=True)
         tomo_paths_odd = [str(p) for p in tmp['tomo_paths_odd']]
         tomo_paths_even = [str(p) for p in tmp['tomo_paths_even']]
         mean = tmp['mean']
@@ -70,7 +73,10 @@ def load(cls, path):
         sample_shape = tmp['sample_shape']
         shuffle = tmp['shuffle']
         coords = tmp['coords']
-        tilt_axis = tmp['tilt_axis']
+        if isinstance(tmp['tilt_axis'], np.ndarray):
+            tilt_axis = None
+        else:
+            tilt_axis = tmp['tilt_axis']
 
         ds = cls(tomo_paths_odd=tomo_paths_odd,
                  tomo_paths_even=tomo_paths_even,
@@ -131,11 +137,12 @@ def create_random_coords(self, z, y, x, n_samples):
 
     def augment(self, x, y):
         if self.tilt_axis is not None:
-            rot_k = np.random.randint(0, 4, x.shape[0])
+            if self.sample_shape[0] == self.sample_shape[1] and \
+                    self.sample_shape[0] == self.sample_shape[2]:
+                rot_k = np.random.randint(0, 4, 1)
 
-            for i in range(x.shape[0]):
-                x[i,...,0] = np.rot90(x[i,...,0], k=rot_k[i], axes=self.rot_axes)
-                y[i,...,0] = np.rot90(y[i,...,0], k=rot_k[i], axes=self.rot_axes)
+                x[...,0] = np.rot90(x[...,0], k=rot_k, axes=self.rot_axes)
+                y[...,0] = np.rot90(y[...,0], k=rot_k, axes=self.rot_axes)
 
 
         if np.random.rand() > 0.5:
@@ -157,7 +164,6 @@ def __getitem__(self, idx):
         odd_subvolume = self.tomos_odd[tomo_index].data[z:z + self.sample_shape[0],
                         y:y + self.sample_shape[1],
                         x:x + self.sample_shape[2]]
-
         return self.augment(np.array(even_subvolume)[..., np.newaxis], np.array(odd_subvolume)[..., np.newaxis])
 
     def __iter__(self):