update for cropping generator

vanvalenlab · Jul 14, 2020 · cfa7fd5 · cfa7fd5
1 parent 2ee399d
commit cfa7fd5
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Showing 2 changed files with 2 additions and 40 deletions.
diff --git a/caliban_toolbox/build.py b/caliban_toolbox/build.py
@@ -59,35 +59,12 @@ def pad_image_stack(images, crop_size):
         return new_images
 
 
-def pad_image_edge_crops(images, crop_size):
-    """Add padding to an image to enable additional edge crops to be generated
-
-    Args:
-        images: array of images to crop
-        crop_size: size of crops that will be produced
-
-    Returns:
-        np.array: padded image
-    """
-    row_offset, col_offset = int(crop_size[0] / 2), int(crop_size[1] / 2)
-
-    padded_images = np.zeros((images.shape[0], images.shape[1] + crop_size[0],
-                              images.shape[2] + crop_size[1], images.shape[3]))
-
-    padded_images[:, row_offset:-row_offset, col_offset:-col_offset, :] = images
-
-    return padded_images
-
-
-def combine_npz_files(npz_list, resize_ratios, extra_edge_padding=False,
-                      stride_ratio=1, final_size=(256, 256)):
+def combine_npz_files(npz_list, resize_ratios, stride_ratio=1, final_size=(256, 256)):
     """Take a series of NPZ files and combine together into single training NPZ
 
     Args:
         npz_list: list of NPZ files to combine
         resize_ratios: ratio used to resize each NPZ if data is of different resolutions
-        extra_edge_padding: if True, adds padding equal to half of the crop size on either edge
-            of the image to increase the number of crops produced from the original image
         stride_ratio: amount of overlap between crops (1 is no overlap, 0.5 is half crop size)
         final_size: size of the final crops to be produced
     Returns:
@@ -119,11 +96,7 @@ def combine_npz_files(npz_list, resize_ratios, extra_edge_padding=False,
             current_x = pad_image_stack(images=current_x, crop_size=final_size)
             current_y = pad_image_stack(images=current_y, crop_size=final_size)
 
-            if extra_edge_padding:
-                # create buffer on either edge to increase number of crops
-                current_x = pad_image_edge_crops(images=current_x, crop_size=final_size)
-                current_y = pad_image_edge_crops(images=current_y, crop_size=final_size)
-
+            # create x and y crops
             current_x, _ = tile_image(image=current_x, model_input_shape=final_size,
                                       stride_ratio=stride_ratio)
             current_y, _ = tile_image(image=current_y, model_input_shape=final_size,

diff --git a/caliban_toolbox/build_test.py b/caliban_toolbox/build_test.py
@@ -68,17 +68,6 @@ def test_pad_image_stack():
     assert np.all(padded_stack[:, 0, 0, 0] == tags)
 
 
-def test_pad_image_edge_crops():
-    input_stack = np.zeros((2, 100, 100, 2))
-    tags = [1, 2]
-    input_stack[:, 0, 0, 0] = tags
-    crop_size = (20, 20)
-
-    padded_stack = build.pad_image_edge_crops(images=input_stack, crop_size=crop_size)
-    assert padded_stack.shape == (2, 120, 120, 2)
-    assert np.all(padded_stack[:, 10, 10, 0] == tags)
-
-
 def test_combine_npz_files():
     # NPZ files are appropriate size and resolution
     npz_list = _make_npzs((256, 256), 2)