adding patches

patch2self.py

@@ -8,7 +8,7 @@ def patch2self(data, patch_radius=[1, 1, 1], mask=None):
         # If mask is not specified, use the whole volume
         mask = np.ones_like(data, dtype=bool)[..., 0]
 
-    def _extract_2d_patches(arr, patch_radius=[1, 1, 1]):
+    def _extract_3d_patches(arr, patch_radius=[1, 1, 1]):
 
         if isinstance(patch_radius, int):
             patch_radius = np.ones(3, dtype=int) * patch_radius
@@ -18,7 +18,6 @@ def _extract_2d_patches(arr, patch_radius=[1, 1, 1]):
             patch_radius = np.asarray(patch_radius).astype(int)
         patch_size = 2 * patch_radius + 1
 
-
         dim = arr.shape[-1]
 
         all_patches = []
@@ -39,7 +38,8 @@ def _extract_2d_patches(arr, patch_radius=[1, 1, 1]):
 
         return np.array(all_patches).T
 
-    train = _extract_2d_patches(data, patch_radius=patch_radius)
+    train = _extract_3d_patches(np.pad(data, ((1, 1), (1, 1), (1, 1)))
+        , patch_radius=patch_radius)
     print(train.shape)
 
     print('Patch Extraction Done...')
@@ -59,33 +59,18 @@ def _extract_2d_patches(arr, patch_radius=[1, 1, 1]):
 
         print('Training for resolution: ', patch_radius)
         cur_X = np.reshape(np.concatenate((X1, X2), axis=0),
-                           (train.shape[0]-1,
-                            train.shape[1]*train.shape[2]))
+                           (-1, train.shape[2]))
+
+        Y = train[f, train.shape[1]//2, :]
 
-        Y = np.reshape(train[f, :, :], (1,
-                       train.shape[1]*train.shape[2]))
+        model.fit(cur_X.T[::100], Y.T[::100])
 
-        model.fit(cur_X.T, Y.T)
         del cur_X, Y, X1, X2
         print(' -> Trained to Denoise Volume: ', f)
-
-        theta = np.zeros((data.shape[0], data.shape[1], data.shape[2], 1))
-        for i in range(f, f+1):
-            for k in range(0, theta.shape[2]):
-                for j in range(0, theta.shape[1]):
-                    for l in range(0, theta.shape[0]):
-                        if not mask[l, j, k]:
-                            continue
-                        X = np.reshape(data[l, j, k, :], (data.shape[3], 1))
-                        X1 = X[:i, :]
-                        X2 = X[i+1:, :]
-                        cur_x = np.reshape(np.concatenate((X1, X2), axis=0),
-                                           (1, data.shape[3]-1))
-
-                        cur_y = model.predict(cur_x)
-                        theta[l, j, k, i-f] = cur_y
-        del model
-        denoised_array[..., f] = np.squeeze(theta)
+
+        denoised_array[..., f] = model.predict(cur_X.T).reshape(
+            data.shape[0], data.shape[1], data.shape[2])
+
         print('Denoising Volume ', f, ' Complete...')
 
     denoised_array[mask == 0] = 0