Improving performance of batchgenerators

batchgenerators/augmentations/color_augmentations.py

@@ -13,64 +13,66 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from builtins import range
-from typing import Tuple, Union, Callable
+from typing import Tuple, Callable, Union
 
 import numpy as np
-from batchgenerators.augmentations.utils import general_cc_var_num_channels, illumination_jitter
 
+from batchgenerators.augmentations.utils import general_cc_var_num_channels, illumination_jitter, get_broadcast_axes, \
+    reverse_broadcast
+
+
+def get_augment_contrast_factor(contrast_range: Union[Tuple[float, float], Callable[[], float]],
+                                per_channel: bool,
+                                size: int,
+                                broadcast_size: int):
+    if per_channel:
+        factor = []
+        for _ in range(size):
+            if callable(contrast_range):
+                factor.append(contrast_range())
+            elif contrast_range[0] < 1 and np.random.random() < 0.5:
+                factor.append(np.random.uniform(contrast_range[0], 1))
+            else:
+                factor.append(np.random.uniform(max(contrast_range[0], 1), contrast_range[1]))
 
-def augment_contrast(data_sample: np.ndarray,
-                     contrast_range: Union[Tuple[float, float], Callable[[], float]] = (0.75, 1.25),
-                     preserve_range: bool = True,
-                     per_channel: bool = True,
-                     p_per_channel: float = 1) -> np.ndarray:
-    if not per_channel:
+        factor = reverse_broadcast(np.array(factor), get_broadcast_axes(broadcast_size))
+    else:
         if callable(contrast_range):
             factor = contrast_range()
+        elif contrast_range[0] < 1 and np.random.random() < 0.5:
+            factor = np.random.uniform(contrast_range[0], 1)
         else:
-            if np.random.random() < 0.5 and contrast_range[0] < 1:
-                factor = np.random.uniform(contrast_range[0], 1)
-            else:
-                factor = np.random.uniform(max(contrast_range[0], 1), contrast_range[1])
+            factor = np.random.uniform(max(contrast_range[0], 1), contrast_range[1])
 
-        for c in range(data_sample.shape[0]):
-            if np.random.uniform() < p_per_channel:
-                mn = data_sample[c].mean()
-                if preserve_range:
-                    minm = data_sample[c].min()
-                    maxm = data_sample[c].max()
+    return factor
 
-                data_sample[c] = (data_sample[c] - mn) * factor + mn
 
-                if preserve_range:
-                    data_sample[c][data_sample[c] < minm] = minm
-                    data_sample[c][data_sample[c] > maxm] = maxm
-    else:
-        for c in range(data_sample.shape[0]):
-            if np.random.uniform() < p_per_channel:
-                if callable(contrast_range):
-                    factor = contrast_range()
-                else:
-                    if np.random.random() < 0.5 and contrast_range[0] < 1:
-                        factor = np.random.uniform(contrast_range[0], 1)
-                    else:
-                        factor = np.random.uniform(max(contrast_range[0], 1), contrast_range[1])
-
-                mn = data_sample[c].mean()
-                if preserve_range:
-                    minm = data_sample[c].min()
-                    maxm = data_sample[c].max()
-
-                data_sample[c] = (data_sample[c] - mn) * factor + mn
-
-                if preserve_range:
-                    data_sample[c][data_sample[c] < minm] = minm
-                    data_sample[c][data_sample[c] > maxm] = maxm
+def augment_contrast(data_sample: np.ndarray,
+                     contrast_range: Union[Tuple[float, float], Callable[[], float]] = (0.75, 1.25),
+                     preserve_range: bool = True,
+                     per_channel: bool = True,
+                     p_per_channel: float = 1,
+                     batched=False) -> np.ndarray:
+    mask = np.random.uniform(size=data_sample.shape[:2] if batched else data_sample.shape[0]) < p_per_channel
+    if np.any(mask):
+        workon = data_sample[mask]
+        factor = get_augment_contrast_factor(contrast_range, per_channel, len(workon), workon.ndim)
+        axes = tuple(range(1, workon.ndim))
+        mean = workon.mean(axis=axes, keepdims=True)
+        if preserve_range:
+            minm = workon.min(axis=axes, keepdims=True)
+            maxm = workon.max(axis=axes, keepdims=True)
+
+        data_sample[mask] = workon * factor + mean * (1 - factor)  # writing directly in data_sample
+
+        if preserve_range:
+            np.clip(data_sample[mask], minm, maxm, out=data_sample[mask])
+
     return data_sample
 
 
-def augment_brightness_additive(data_sample, mu:float, sigma:float , per_channel:bool=True, p_per_channel:float=1.):
+def augment_brightness_additive(data_sample, mu: float, sigma: float, per_channel: bool = True,
+                                p_per_channel: float = 1.):
     """
     data_sample must have shape (c, x, y(, z)))
     :param data_sample: 
@@ -80,27 +82,29 @@ def augment_brightness_additive(data_sample, mu:float, sigma:float , per_channel
     :param p_per_channel: 
     :return: 
     """
-    if not per_channel:
-        rnd_nb = np.random.normal(mu, sigma)
-        for c in range(data_sample.shape[0]):
-            if np.random.uniform() <= p_per_channel:
-                data_sample[c] += rnd_nb
+    size = data_sample.shape[0]
+    if per_channel:
+        rnd_nb = np.random.normal(mu, sigma, size=size)
     else:
-        for c in range(data_sample.shape[0]):
-            if np.random.uniform() <= p_per_channel:
-                rnd_nb = np.random.normal(mu, sigma)
-                data_sample[c] += rnd_nb
+        rnd_nb = np.repeat(np.random.normal(mu, sigma), size)
+    rnd_nb[np.random.uniform(size=size) > p_per_channel] = 0.0
+    data_sample += reverse_broadcast(rnd_nb, get_broadcast_axes(data_sample.ndim))
     return data_sample
 
 
-def augment_brightness_multiplicative(data_sample, multiplier_range=(0.5, 2), per_channel=True):
-    multiplier = np.random.uniform(multiplier_range[0], multiplier_range[1])
-    if not per_channel:
-        data_sample *= multiplier
-    else:
-        for c in range(data_sample.shape[0]):
-            multiplier = np.random.uniform(multiplier_range[0], multiplier_range[1])
-            data_sample[c] *= multiplier
+def setup_augment_brightness_multiplicative(per_channel: bool, batched: bool, shape: Tuple[int, ...]):
+    if per_channel:
+        if batched:
+            return shape[:2] + (1,) * (len(shape) - 2)
+        return (shape[0],) + (1,) * (len(shape) - 1)
+    if batched:
+        return (shape[0],) + (1,) * (len(shape) - 1)
+    return (1,) * len(shape)
+
+
+def augment_brightness_multiplicative(data_sample, multiplier_range=(0.5, 2), per_channel=True, batched=False):
+    size = setup_augment_brightness_multiplicative(per_channel, batched, data_sample.shape)
+    data_sample *= np.random.uniform(multiplier_range[0], multiplier_range[1], size=size)
     return data_sample
 
 
@@ -110,38 +114,55 @@ def augment_gamma(data_sample, gamma_range=(0.5, 2), invert_image=False, epsilon
         data_sample = - data_sample
 
     if not per_channel:
-        retain_stats_here = retain_stats() if callable(retain_stats) else retain_stats
-        if retain_stats_here:
+        retain_stats = retain_stats() if callable(retain_stats) else retain_stats
+        if retain_stats:
             mn = data_sample.mean()
             sd = data_sample.std()
-        if np.random.random() < 0.5 and gamma_range[0] < 1:
+        if gamma_range[0] < 1 and np.random.random() < 0.5:
             gamma = np.random.uniform(gamma_range[0], 1)
         else:
             gamma = np.random.uniform(max(gamma_range[0], 1), gamma_range[1])
         minm = data_sample.min()
         rnge = data_sample.max() - minm
         data_sample = np.power(((data_sample - minm) / float(rnge + epsilon)), gamma) * rnge + minm
-        if retain_stats_here:
-            data_sample = data_sample - data_sample.mean()
-            data_sample = data_sample / (data_sample.std() + 1e-8) * sd
-            data_sample = data_sample + mn
+        if retain_stats:
+            data_sample -= data_sample.mean()
+            data_sample *= sd / (data_sample.std() + 1e-8)
+            data_sample += mn
     else:
-        for c in range(data_sample.shape[0]):
-            retain_stats_here = retain_stats() if callable(retain_stats) else retain_stats
-            if retain_stats_here:
-                mn = data_sample[c].mean()
-                sd = data_sample[c].std()
-            if np.random.random() < 0.5 and gamma_range[0] < 1:
-                gamma = np.random.uniform(gamma_range[0], 1)
+        shape_0 = data_sample.shape[0]
+        gamma = []
+        gamma_l = max(gamma_range[0], 1)
+        for i in range(shape_0):
+            if gamma_range[0] < 1 and np.random.random() < 0.5:
+                gamma.append(np.random.uniform(gamma_range[0], 1))
             else:
-                gamma = np.random.uniform(max(gamma_range[0], 1), gamma_range[1])
-            minm = data_sample[c].min()
-            rnge = data_sample[c].max() - minm
-            data_sample[c] = np.power(((data_sample[c] - minm) / float(rnge + epsilon)), gamma) * float(rnge + epsilon) + minm
-            if retain_stats_here:
-                data_sample[c] = data_sample[c] - data_sample[c].mean()
-                data_sample[c] = data_sample[c] / (data_sample[c].std() + 1e-8) * sd
-                data_sample[c] = data_sample[c] + mn
+                gamma.append(np.random.uniform(gamma_l, gamma_range[1]))
+        gamma = np.array(gamma)
+
+        axes = tuple(range(1, data_sample.ndim))
+
+        if callable(retain_stats):
+            retain_stats = [retain_stats() for _ in range(shape_0)]
+        else:
+            retain_stats = [retain_stats] * shape_0
+        retain_stats_here = any(retain_stats)
+        if retain_stats_here:
+            mn = data_sample[retain_stats].mean(axis=axes, keepdims=True)
+            sd = data_sample[retain_stats].mean(axis=axes, keepdims=True)
+
+        minm = data_sample.min(axis=axes, keepdims=True)
+        rnge = data_sample.max(axis=axes, keepdims=True) - minm + epsilon
+
+        broadcast_axes = get_broadcast_axes(data_sample.ndim)
+        gamma = reverse_broadcast(gamma, broadcast_axes)
+        data_sample = np.power((data_sample - minm) / rnge, gamma) * rnge + minm
+
+        if retain_stats_here:
+            data_sample[retain_stats] -= data_sample[retain_stats].mean(axis=axes, keepdims=True)
+            data_sample[retain_stats] *= sd / (data_sample[retain_stats].std(axis=axes, keepdims=True) + 1e-8)
+            data_sample[retain_stats] += mn
+
     if invert_image:
         data_sample = - data_sample
     return data_sample

batchgenerators/augmentations/crop_and_pad_augmentations.py

@@ -13,9 +13,9 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from builtins import range
 import numpy as np
 from batchgenerators.augmentations.utils import pad_nd_image
+from typing import Union, Sequence
 
 
 def center_crop(data, crop_size, seg=None):
@@ -30,28 +30,24 @@ def get_lbs_for_random_crop(crop_size, data_shape, margins):
     :param margins:
     :return:
     """
-    lbs = []
-    for i in range(len(data_shape) - 2):
-        if data_shape[i+2] - crop_size[i] - margins[i] > margins[i]:
-            lbs.append(np.random.randint(margins[i], data_shape[i+2] - crop_size[i] - margins[i]))
-        else:
-            lbs.append((data_shape[i+2] - crop_size[i]) // 2)
-    return lbs
+    new_shape = data_shape - crop_size
+    mask = new_shape > 2 * margins
+    new_shape[mask] = np.random.randint(margins[mask], new_shape[mask] - margins[mask])
+    new_shape[~mask] //= 2
+    return new_shape
 
 
 def get_lbs_for_center_crop(crop_size, data_shape):
     """
     :param crop_size:
-    :param data_shape: (b,c,x,y(,z)) must be the whole thing!
+    :param data_shape: (b,c,x,y(,z)) must be the only x,y(,z)!
     :return:
     """
-    lbs = []
-    for i in range(len(data_shape) - 2):
-        lbs.append((data_shape[i + 2] - crop_size[i]) // 2)
-    return lbs
+    return (data_shape - crop_size) // 2
 
 
-def crop(data, seg=None, crop_size=128, margins=(0, 0, 0), crop_type="center",
+def crop(data: Union[Sequence[np.ndarray], np.ndarray], seg: Union[Sequence[np.ndarray], np.ndarray] = None,
+         crop_size=128, margins=(0, 0, 0), crop_type="center",
          pad_mode='constant', pad_kwargs={'constant_values': 0},
          pad_mode_seg='constant', pad_kwargs_seg={'constant_values': 0}):
     """
@@ -69,44 +65,39 @@ def crop(data, seg=None, crop_size=128, margins=(0, 0, 0), crop_type="center",
     :param crop_type: random or center
     :return:
     """
-    if not isinstance(data, (list, tuple, np.ndarray)):
-        raise TypeError("data has to be either a numpy array or a list")
-
-    data_shape = tuple([len(data)] + list(data[0].shape))
+    data_shape = (len(data),) + data[0].shape
     data_dtype = data[0].dtype
     dim = len(data_shape) - 2
 
     if seg is not None:
-        seg_shape = tuple([len(seg)] + list(seg[0].shape))
+        seg_shape = (len(seg),) + seg[0].shape
         seg_dtype = seg[0].dtype
 
-        if not isinstance(seg, (list, tuple, np.ndarray)):
-            raise TypeError("data has to be either a numpy array or a list")
-
-        assert all([i == j for i, j in zip(seg_shape[2:], data_shape[2:])]), "data and seg must have the same spatial " \
-                                                                             "dimensions. Data: %s, seg: %s" % \
-                                                                             (str(data_shape), str(seg_shape))
+        assert np.array_equal(seg_shape[2:], data_shape[2:]), "data and seg must have the same spatial dimensions. " \
+                                                              f"Data: {data_shape}, seg: {seg_shape}"
 
     if type(crop_size) not in (tuple, list, np.ndarray):
-        crop_size = [crop_size] * dim
+        crop_size = (crop_size,) * dim
     else:
-        assert len(crop_size) == len(
-            data_shape) - 2, "If you provide a list/tuple as center crop make sure it has the same dimension as your " \
-                             "data (2d/3d)"
+        assert len(crop_size) == dim, ("If you provide a list/tuple as center crop make sure it has the same dimension "
+                                       "as your data (2d/3d)")
+    crop_size = np.asarray(crop_size)
 
     if not isinstance(margins, (np.ndarray, tuple, list)):
-        margins = [margins] * dim
+        margins = (margins,) * dim
+    margins = np.asarray(margins)
 
-    data_return = np.zeros([data_shape[0], data_shape[1]] + list(crop_size), dtype=data_dtype)
+    data_return = np.zeros((data_shape[0], data_shape[1], *crop_size), dtype=data_dtype)
     if seg is not None:
-        seg_return = np.zeros([seg_shape[0], seg_shape[1]] + list(crop_size), dtype=seg_dtype)
+        seg_return = np.zeros((seg_shape[0], seg_shape[1], *crop_size), dtype=seg_dtype)
     else:
         seg_return = None
 
     for b in range(data_shape[0]):
-        data_shape_here = [data_shape[0]] + list(data[b].shape)
+        data_first_dim = data[b].shape[0]
+        data_shape_here = np.array(data[b].shape[1:])
         if seg is not None:
-            seg_shape_here = [seg_shape[0]] + list(seg[b].shape)
+            seg_first_dim = seg[b].shape[0]
 
         if crop_type == "center":
             lbs = get_lbs_for_center_crop(crop_size, data_shape_here)
@@ -115,22 +106,25 @@ def crop(data, seg=None, crop_size=128, margins=(0, 0, 0), crop_type="center",
         else:
             raise NotImplementedError("crop_type must be either center or random")
 
-        need_to_pad = [[0, 0]] + [[abs(min(0, lbs[d])),
-                                   abs(min(0, data_shape_here[d + 2] - (lbs[d] + crop_size[d])))]
-                                  for d in range(dim)]
+        zero = np.zeros(dim, dtype=int)
+        temp1 = np.abs(np.minimum(lbs, zero))
+        lbs_plus_crop_size = lbs + crop_size
+        temp2 = np.abs(np.minimum(zero, data_shape_here - lbs_plus_crop_size))
+        need_to_pad = ((0, 0),) + tuple(zip(temp1, temp2))
+        need_to_pad = np.array(need_to_pad)
 
         # we should crop first, then pad -> reduces i/o for memmaps, reduces RAM usage and improves speed
-        ubs = [min(lbs[d] + crop_size[d], data_shape_here[d+2]) for d in range(dim)]
-        lbs = [max(0, lbs[d]) for d in range(dim)]
+        ubs = np.minimum(data_shape_here, lbs_plus_crop_size)
+        lbs = np.maximum(zero, lbs)
 
-        slicer_data = [slice(0, data_shape_here[1])] + [slice(lbs[d], ubs[d]) for d in range(dim)]
-        data_cropped = data[b][tuple(slicer_data)]
+        slicer_data = (slice(0, data_first_dim), *[slice(lbs[d], ubs[d]) for d in range(dim)])
+        data_cropped = data[b][slicer_data]
 
         if seg_return is not None:
-            slicer_seg = [slice(0, seg_shape_here[1])] + [slice(lbs[d], ubs[d]) for d in range(dim)]
-            seg_cropped = seg[b][tuple(slicer_seg)]
+            slicer_data = (slice(0, seg_first_dim),) + slicer_data[1:]
+            seg_cropped = seg[b][slicer_data]
 
-        if any([i > 0 for j in need_to_pad for i in j]):
+        if np.any(need_to_pad):
             data_return[b] = np.pad(data_cropped, need_to_pad, pad_mode, **pad_kwargs)
             if seg_return is not None:
                 seg_return[b] = np.pad(seg_cropped, need_to_pad, pad_mode_seg, **pad_kwargs_seg)