batchgeneratorsv2 0.3.0__tar.gz → 0.3.3__tar.gz

{batchgeneratorsv2-0.3.0 → batchgeneratorsv2-0.3.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: batchgeneratorsv2
-Version: 0.3.0
+Version: 0.3.3
 Summary: Batchgenerators but better
 Author: Helmholtz Imaging Applied Computer Vision Lab
 Author-email: Fabian Isensee <f.isensee@dkfz-heidelberg.de>
@@ -220,7 +220,6 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: torch>=2.0.0
 Requires-Dist: numpy
-Requires-Dist: fft-conv-pytorch
 Requires-Dist: batchgenerators>=0.25
 Dynamic: license-file
 

batchgeneratorsv2-0.3.3/batchgeneratorsv2/helpers/fft_conv.py

@@ -0,0 +1,149 @@
+from typing import Iterable, Tuple, Union
+
+import torch
+import torch.nn.functional as f
+from torch import Tensor, nn
+from torch.fft import irfftn, rfftn
+from math import ceil, floor
+
+
+# Taken from here: https://github.com/vcasellesb/fft-conv-pytorch/tree/non-tup-slice-fix. THANK YOU!
+# Original codebase is here: https://github.com/fkodom/fft-conv-pytorch -> unfortunately was not updated for pytorch 2.9.
+
+
+def complex_matmul(a: Tensor, b: Tensor, groups: int = 1) -> Tensor:
+    """Multiplies two complex-valued tensors."""
+    # Scalar matrix multiplication of two tensors, over only the first channel
+    # dimensions. Dimensions 3 and higher will have the same shape after multiplication.
+    # We also allow for "grouped" multiplications, where multiple sections of channels
+    # are multiplied independently of one another (required for group convolutions).
+    a = a.view(a.size(0), groups, -1, *a.shape[2:])
+    b = b.view(groups, -1, *b.shape[1:])
+
+    a = torch.movedim(a, 2, a.dim() - 1).unsqueeze(-2)
+    b = torch.movedim(b, (1, 2), (b.dim() - 1, b.dim() - 2))
+
+    # complex value matrix multiplication
+    real = a.real @ b.real - a.imag @ b.imag
+    imag = a.imag @ b.real + a.real @ b.imag
+    real = torch.movedim(real, real.dim() - 1, 2).squeeze(-1)
+    imag = torch.movedim(imag, imag.dim() - 1, 2).squeeze(-1)
+    c = torch.zeros(real.shape, dtype=torch.complex64, device=a.device)
+    c.real, c.imag = real, imag
+
+    return c.view(c.size(0), -1, *c.shape[3:])
+
+
+def to_ntuple(val: Union[int, Iterable[int]], n: int) -> Tuple[int, ...]:
+    """Casts to a tuple with length 'n'.  Useful for automatically computing the
+    padding and stride for convolutions, where users may only provide an integer.
+
+    Args:
+        val: (Union[int, Iterable[int]]) Value to cast into a tuple.
+        n: (int) Desired length of the tuple
+
+    Returns:
+        (Tuple[int, ...]) Tuple of length 'n'
+    """
+    if isinstance(val, Iterable):
+        out = tuple(val)
+        if len(out) == n:
+            return out
+        else:
+            raise ValueError(f"Cannot cast tuple of length {len(out)} to length {n}.")
+    else:
+        return n * (val,)
+
+
+def fft_conv(
+    signal: Tensor,
+    kernel: Tensor,
+    bias: Tensor = None,
+    padding: Union[int, Iterable[int], str] = 0,
+    padding_mode: str = "constant",
+    stride: Union[int, Iterable[int]] = 1,
+    dilation: Union[int, Iterable[int]] = 1,
+    groups: int = 1,
+) -> Tensor:
+    """Performs N-d convolution of Tensors using a fast fourier transform, which
+    is very fast for large kernel sizes. Also, optionally adds a bias Tensor after
+    the convolution (in order ot mimic the PyTorch direct convolution).
+
+    Args:
+        signal: (Tensor) Input tensor to be convolved with the kernel.
+        kernel: (Tensor) Convolution kernel.
+        bias: (Tensor) Bias tensor to add to the output.
+        padding: (Union[int, Iterable[int], str) If int, Number of zero samples to pad then
+            input on the last dimension. If str, "same" supported to pad input for size preservation.
+        padding_mode: (str) Padding mode to use from {constant, reflection, replication}.
+                      reflection not available for 3d.
+        stride: (Union[int, Iterable[int]) Stride size for computing output values.
+        dilation: (Union[int, Iterable[int]) Dilation rate for the kernel.
+        groups: (int) Number of groups for the convolution.
+
+    Returns:
+        (Tensor) Convolved tensor
+    """
+
+    # Cast padding, stride & dilation to tuples.
+    n = signal.ndim - 2
+    stride_ = to_ntuple(stride, n=n)
+    dilation_ = to_ntuple(dilation, n=n)
+    if isinstance(padding, str):
+        if padding == "same":
+            if stride != 1 or dilation != 1:
+                raise ValueError("stride must be 1 for padding='same'.")
+            padding_ = [(k - 1) / 2 for k in kernel.shape[2:]]
+        # else:
+        #     raise ValueError(f"Padding mode {padding} not supported.")
+    else:
+        padding_ = to_ntuple(padding, n=n)
+
+    # internal dilation offsets
+    offset = torch.zeros(1, 1, *dilation_, device=signal.device, dtype=signal.dtype)
+    offset[(slice(None), slice(None), *((0,) * n))] = 1.0
+
+    # correct the kernel by cutting off unwanted dilation trailing zeros
+    cutoff = tuple(slice(None, -d + 1 if d != 1 else None) for d in dilation_)
+
+    # pad the kernel internally according to the dilation parameters
+    kernel = torch.kron(kernel, offset)[(slice(None), slice(None)) + cutoff]
+
+    # Pad the input signal & kernel tensors (round to support even sized convolutions)
+    signal_padding = [r(p) for p in padding_[::-1] for r in (floor, ceil)]
+    signal = f.pad(signal, signal_padding, mode=padding_mode)
+
+    # Because PyTorch computes a *one-sided* FFT, we need the final dimension to
+    # have *even* length.  Just pad with one more zero if the final dimension is odd.
+    signal_size = signal.size()  # original signal size without padding to even
+    if signal.size(-1) % 2 != 0:
+        signal = f.pad(signal, [0, 1])
+
+    kernel_padding = [
+        pad
+        for i in reversed(range(2, signal.ndim))
+        for pad in [0, signal.size(i) - kernel.size(i)]
+    ]
+    padded_kernel = f.pad(kernel, kernel_padding)
+
+    # Perform fourier convolution -- FFT, matrix multiply, then IFFT
+    signal_fr = rfftn(signal.float(), dim=tuple(range(2, signal.ndim)))
+    kernel_fr = rfftn(padded_kernel.float(), dim=tuple(range(2, signal.ndim)))
+
+    kernel_fr.imag *= -1
+    output_fr = complex_matmul(signal_fr, kernel_fr, groups=groups)
+    output = irfftn(output_fr, dim=tuple(range(2, signal.ndim)))
+
+    # Remove extra padded values
+    crop_slices = (slice(None), slice(None)) + tuple(
+        slice(0, (signal_size[i] - kernel.size(i) + 1), stride_[i - 2])
+        for i in range(2, signal.ndim)
+    )
+    output = output[crop_slices].contiguous()
+
+    # Optionally, add a bias term before returning.
+    if bias is not None:
+        bias_shape = tuple([1, -1] + (signal.ndim - 2) * [1])
+        output += bias.view(bias_shape)
+
+    return output

{batchgeneratorsv2-0.3.0 → batchgeneratorsv2-0.3.3}/batchgeneratorsv2/transforms/intensity/brightness.py

@@ -38,42 +38,58 @@ class BrightnessAdditiveTransform(ImageOnlyTransform):
     """
     Adds random additive brightness noise sampled from a Gaussian distribution (mu, sigma).
 
-    Supports per-channel brightness sampling or shared brightness across all channels.
+    Supports either synchronized brightness shift across all channels or per-channel brightness shift.
 
     Args:
         mu (float): Mean of the Gaussian used to sample brightness shifts.
         sigma (float): Standard deviation of the Gaussian.
-        per_channel (bool): If True, brightness shifts are sampled separately per channel.
+        synchronize_channels (bool): If True, brightness shifts are shared across all channels.
         p_per_channel (float): Probability to apply the brightness shift to each channel.
     """
 
     def __init__(self,
                  mu: float,
                  sigma: float,
-                 per_channel: bool = True,
+                 synchronize_channels: bool = True,  # Changed to synchronize_channels
                  p_per_channel: float = 1.0):
         super().__init__()
         self.mu = mu
         self.sigma = sigma
-        self.per_channel = per_channel
+        self.synchronize_channels = synchronize_channels  # Now it's being used
         self.p_per_channel = p_per_channel
 
-    def get_parameters(self, image: torch.Tensor, **kwargs) -> dict:
-        C = image.shape[0]
-        apply_channel = [np.random.rand() < self.p_per_channel for _ in range(C)]
+    def get_parameters(self, **data_dict) -> dict:
+        img = data_dict["image"]
+        c = img.shape[0]
+        apply_to_channel = (torch.rand(c, device=img.device) < self.p_per_channel).nonzero(as_tuple=False).flatten()
+
+        if len(apply_to_channel) == 0:
+            return {"apply_to_channel": apply_to_channel, "shift": None}
 
-        if self.per_channel:
-            brightness = [np.random.normal(self.mu, self.sigma) if apply else None for apply in apply_channel]
+        # Apply either synchronized or per-channel brightness shift
+        if self.synchronize_channels:
+            shift_value = float(sample_scalar((self.mu, self.sigma), image=img, channel=None))
+            shift = torch.full((c,), shift_value, device=img.device)
         else:
-            global_brightness = np.random.normal(self.mu, self.sigma)
-            brightness = [global_brightness if apply else None for apply in apply_channel]
+            shift = torch.empty(c, device=img.device).normal_(float(self.mu), float(self.sigma))
 
-        return {'brightness': brightness}
+        return {"apply_to_channel": apply_to_channel, "shift": shift}
 
     def _apply_to_image(self, img: torch.Tensor, **params) -> torch.Tensor:
-        for c, b in enumerate(params['brightness']):
-            if b is not None:
-                img[c].add_(float(b))
+        if params["shift"] is None:
+            return img
+
+        apply_idx = params["apply_to_channel"]
+        if apply_idx.numel() == 0:
+            return img
+
+        shift = params["shift"]
+        # Build full per-channel shift vector; non-selected channels get shift 0
+        shift_full = torch.zeros((img.shape[0],), device=img.device, dtype=img.dtype)
+        shift_full[apply_idx] = shift[apply_idx]
+
+        view_shape = (img.shape[0],) + (1,) * (img.ndim - 1)
+        img.add_(shift_full.view(view_shape))
         return img
 
 
@@ -84,7 +100,8 @@ if __name__ == '__main__':
     os.environ['OMP_NUM_THREADS'] = '1'
     torch.set_num_threads(1)
 
-    mbt = MultiplicativeBrightnessTransform((0.5, 2.), False, 1)
+    # mbt = BrightnessAdditiveTransform(0, 0.5,True, 1)
+    mbt = MultiplicativeBrightnessTransform((0.5, 2),False, 1)
 
     times_torch = []
     for _ in range(1000):

{batchgeneratorsv2-0.3.0 → batchgeneratorsv2-0.3.3}/batchgeneratorsv2/transforms/intensity/contrast.py

@@ -26,44 +26,70 @@ class BGContrast():
         return self.__class__.__name__ + f"(contrast_range={self.contrast_range})"
 
 
+import torch
+from batchgeneratorsv2.helpers.scalar_type import RandomScalar, sample_scalar
+from batchgeneratorsv2.transforms.base.basic_transform import ImageOnlyTransform
+
+
 class ContrastTransform(ImageOnlyTransform):
-    def __init__(self, contrast_range: RandomScalar, preserve_range: bool, synchronize_channels: bool, p_per_channel: float = 1):
+    def __init__(self, contrast_range: RandomScalar, preserve_range: bool, synchronize_channels: bool, p_per_channel: float = 1.0):
         super().__init__()
         self.contrast_range = contrast_range
         self.preserve_range = preserve_range
         self.synchronize_channels = synchronize_channels
-        self.p_per_channel = p_per_channel
+        self.p_per_channel = float(p_per_channel)
 
     def get_parameters(self, **data_dict) -> dict:
-        shape = data_dict['image'].shape
-        apply_to_channel = torch.where(torch.rand(shape[0]) < self.p_per_channel)[0]
-        if self.synchronize_channels:
-            multipliers = torch.Tensor([sample_scalar(self.contrast_range, image=data_dict['image'], channel=None)] * len(apply_to_channel))
+        img = data_dict["image"]
+        c = img.shape[0]
+
+        # sample on correct device
+        apply_idx = (torch.rand(c, device=img.device) < self.p_per_channel).nonzero(as_tuple=False).flatten()
+        n = apply_idx.numel()
+
+        if n == 0:
+            multipliers = None
+        elif self.synchronize_channels:
+            m = float(sample_scalar(self.contrast_range, image=img, channel=None))
+            multipliers = torch.full((n,), m, device=img.device, dtype=img.dtype)
         else:
-            multipliers = torch.Tensor([sample_scalar(self.contrast_range, image=data_dict['image'], channel=c) for c in apply_to_channel])
-        return {
-            'apply_to_channel': apply_to_channel,
-            'multipliers': multipliers
-        }
+            # Still a Python loop because sample_scalar is scalar-by-scalar
+            # Use .tolist() to avoid iterating tensor scalars in Python
+            ms = [sample_scalar(self.contrast_range, image=img, channel=int(ch)) for ch in apply_idx.tolist()]
+            multipliers = torch.as_tensor(ms, device=img.device, dtype=img.dtype)
+
+        return {"apply_to_channel": apply_idx, "multipliers": multipliers}
 
     def _apply_to_image(self, img: torch.Tensor, **params) -> torch.Tensor:
-        if len(params['apply_to_channel']) == 0:
+        idx = params["apply_to_channel"]
+        multipliers = params["multipliers"]
+        if multipliers is None or idx.numel() == 0:
             return img
-        # array notation is not faster, let's leave it like this
-        for i in range(len(params['apply_to_channel'])):
-            c = params['apply_to_channel'][i]
-            mean = img[c].mean()
-            if self.preserve_range:
-                minm = img[c].min()
-                maxm = img[c].max()
-
-            # this is faster than having it in one line because this circumvents reallocating memory
-            img[c] -= mean
-            img[c] *= params['multipliers'][i]
-            img[c] += mean
-
-            if self.preserve_range:
-                img[c].clamp_(minm, maxm)
+
+        if self.preserve_range:
+            for i in range(idx.numel()):
+                c = int(idx[i])
+                m = multipliers[i]
+
+                x = img[c]
+                mean = x.mean()
+                minm = x.min()
+                maxm = x.max()
+
+                x.sub_(mean)
+                x.mul_(m)
+                x.add_(mean)
+                x.clamp_(minm, maxm)
+        else:
+            for i in range(idx.numel()):
+                c = int(idx[i])
+                m = multipliers[i]
+
+                x = img[c]
+                mean = x.mean()
+                x.sub_(mean)
+                x.mul_(m)
+                x.add_(mean)
 
         return img
 

batchgeneratorsv2-0.3.3/batchgeneratorsv2/transforms/intensity/gamma.py

@@ -0,0 +1,135 @@
+from typing import Optional
+import torch
+
+from batchgeneratorsv2.helpers.scalar_type import RandomScalar, sample_scalar
+from batchgeneratorsv2.transforms.base.basic_transform import ImageOnlyTransform
+
+
+class GammaTransform(ImageOnlyTransform):
+    def __init__(self,
+                 gamma: RandomScalar,
+                 p_invert_image: float,
+                 synchronize_channels: bool,
+                 p_per_channel: float,
+                 p_retain_stats: float):
+        super().__init__()
+        self.gamma = gamma
+        self.p_invert_image = float(p_invert_image)
+        self.synchronize_channels = synchronize_channels
+        self.p_per_channel = float(p_per_channel)
+        self.p_retain_stats = float(p_retain_stats)
+
+    def get_parameters(self, **data_dict) -> dict:
+        img: torch.Tensor = data_dict["image"]
+        c = img.shape[0]
+        device = img.device
+        dtype = img.dtype
+
+        apply_idx = (torch.rand(c, device=device) < self.p_per_channel).nonzero(as_tuple=False).flatten()
+        n = apply_idx.numel()
+        if n == 0:
+            return {"apply_to_channel": apply_idx,
+                    "retain_stats": None,
+                    "invert_image": None,
+                    "gamma": None}
+
+        retain_stats = (torch.rand(n, device=device) < self.p_retain_stats)
+        invert_image = (torch.rand(n, device=device) < self.p_invert_image)
+
+        if self.synchronize_channels:
+            g = float(sample_scalar(self.gamma, image=img, channel=None))
+            gamma = torch.full((n,), g, device=device, dtype=dtype)
+        else:
+            # sample_scalar is scalar-based; keep loop but avoid tensor scalar iteration
+            gs = [float(sample_scalar(self.gamma, image=img, channel=int(ch))) for ch in apply_idx.tolist()]
+            gamma = torch.as_tensor(gs, device=device, dtype=dtype)
+
+        return {
+            "apply_to_channel": apply_idx,
+            "retain_stats": retain_stats,
+            "invert_image": invert_image,
+            "gamma": gamma,
+        }
+
+    def _apply_to_image(self, img: torch.Tensor, **params) -> torch.Tensor:
+        idx: torch.Tensor = params["apply_to_channel"]
+        if idx.numel() == 0:
+            return img
+
+        retain_stats: torch.Tensor = params["retain_stats"]
+        invert_image: torch.Tensor = params["invert_image"]
+        gamma: torch.Tensor = params["gamma"]
+
+        # constants
+        eps = 1e-7
+
+        # Loop over selected channels (good for small C)
+        for k in range(idx.numel()):
+            c = int(idx[k])
+            r = bool(retain_stats[k])
+            inv = bool(invert_image[k])
+            g = gamma[k]
+
+            x = img[c]
+
+            if inv:
+                x.mul_(-1)
+
+            if r:
+                mean = x.mean()
+                std = x.std()
+
+            minm = x.min()
+            maxm = x.max()
+            rnge = maxm - minm
+            denom = torch.clamp(rnge, min=eps)
+
+            # In-place gamma: x = (((x - min) / denom) ** g) * rnge + min
+            x.sub_(minm)
+            x.div_(denom)
+            x.pow_(g)
+            x.mul_(rnge)
+            x.add_(minm)
+
+            if r:
+                mn_here = x.mean()
+                std_here = x.std()
+                x.sub_(mn_here)
+                x.mul_(std / torch.clamp(std_here, min=eps))
+                x.add_(mean)
+
+            if inv:
+                x.mul_(-1)
+
+        return img
+
+
+
+if __name__ == '__main__':
+    from time import time
+    import numpy as np
+    import os
+
+    os.environ['OMP_NUM_THREADS'] = '1'
+    torch.set_num_threads(1)
+
+    mbt = GammaTransform((0.7, 1.5), 0, False, 1, 1)
+
+    times_torch = []
+    for _ in range(100):
+        data_dict = {'image': torch.ones((2, 128, 192, 64))}
+        st = time()
+        out = mbt(**data_dict)
+        times_torch.append(time() - st)
+    print('torch', np.mean(times_torch))
+
+    from batchgenerators.transforms.color_transforms import GammaTransform as BGGamma
+
+    gnt_bg = BGGamma((0.7, 1.5), False, True, retain_stats=True, p_per_sample=1)
+    times_bg = []
+    for _ in range(100):
+        data_dict = {'data': np.ones((1, 2, 128, 192, 64))}
+        st = time()
+        out = gnt_bg(**data_dict)
+        times_bg.append(time() - st)
+    print('bg', np.mean(times_bg))

batchgeneratorsv2-0.3.3/batchgeneratorsv2/transforms/intensity/gaussian_noise.py

@@ -0,0 +1,104 @@
+from typing import Tuple
+import torch
+
+from batchgeneratorsv2.helpers.scalar_type import RandomScalar, sample_scalar
+from batchgeneratorsv2.transforms.base.basic_transform import ImageOnlyTransform
+
+
+class GaussianNoiseTransform(ImageOnlyTransform):
+    def __init__(self,
+                 noise_variance: RandomScalar = (0, 0.1),
+                 p_per_channel: float = 1.,
+                 synchronize_channels: bool = False):
+        super().__init__()
+        self.noise_variance = noise_variance
+        self.p_per_channel = p_per_channel
+        self.synchronize_channels = synchronize_channels
+
+    def get_parameters(self, **data_dict) -> dict:
+        img = data_dict["image"]
+        c = img.shape[0]
+
+        # bool mask on same device as image
+        apply = torch.rand(c, device=img.device) < self.p_per_channel
+
+        # store also count / indices to avoid recomputing later
+        idx = apply.nonzero(as_tuple=False).flatten()
+        n = idx.numel()
+
+        if n == 0:
+            sigmas = None
+        elif self.synchronize_channels:
+            sigmas = sample_scalar(self.noise_variance, img)
+        else:
+            # still uses sample_scalar, but avoids list->cat in _apply
+            # if sample_scalar is cheap, this is fine; otherwise see note below
+            sigmas = [sample_scalar(self.noise_variance, img) for _ in range(n)]
+
+        return {"apply_mask": apply, "apply_idx": idx, "num_apply": n, "sigmas": sigmas}
+
+    def _apply_to_image(self, img: torch.Tensor, **params) -> torch.Tensor:
+        n = params["num_apply"]
+        if n == 0:
+            return img
+
+        idx = params["apply_idx"]
+        spatial = img.shape[1:]
+        device = img.device
+        dtype = img.dtype
+
+        sigmas = params["sigmas"]
+
+        if sigmas is None:
+            return img
+
+        # Create noise only for selected channels
+        if not self.synchronize_channels:
+            # vectorize per-channel sigma by creating a tensor of shape (n, 1, 1, ...)
+            # list->tensor is small (n floats), then broadcast
+            sigma_t = torch.as_tensor(sigmas, device=device, dtype=dtype)
+            view_shape = (n,) + (1,) * len(spatial)
+            sigma_t = sigma_t.view(view_shape)
+
+            noise = torch.empty((n, *spatial), device=device, dtype=dtype).normal_()
+            noise.mul_(sigma_t)
+        else:
+            sigma = sigmas
+            noise = torch.empty((n, *spatial), device=device, dtype=dtype).normal_(mean=0.0, std=float(sigma))
+
+        # Advanced indexing (img[idx]) returns a copy, so use indexed assignment
+        # to make sure modifications are written back to img.
+        img[idx] += noise
+        return img
+    
+
+if __name__ == "__main__":
+    from time import time
+    import numpy as np
+
+    os.environ['OMP_NUM_THREADS'] = '1'
+    torch.set_num_threads(1)
+
+    gnt = GaussianNoiseTransform((0, 0.1), 1, False)
+
+    times = []
+    for _ in range(1000):
+        data_dict = {'image': torch.ones((2, 32, 32, 32))}
+        st = time()
+        out = gnt(**data_dict)
+        times.append(time() - st)
+    print('torch', np.mean(times))
+
+    from batchgenerators.transforms.noise_transforms import GaussianNoiseTransform
+
+    gnt_bg = GaussianNoiseTransform((0, 0.1), 1, 1, True)
+
+    times = []
+    for _ in range(1000):
+        data_dict = {'data': np.ones((1, 2, 32, 32, 32))}
+        st = time()
+        out = gnt_bg(**data_dict)
+        times.append(time() - st)
+
+    print('bg', np.mean(times))
+    # torch is 2.5x faster

{batchgeneratorsv2-0.3.0 → batchgeneratorsv2-0.3.3}/batchgeneratorsv2/transforms/intensity/random_clip.py

@@ -67,12 +67,11 @@ class CutOffOutliersTransform(ImageOnlyTransform):
             if retain_std[c]:
                 orig_std = img_c.std()
 
-            # Use numpy only to calculate percentiles
-            img_c_np = img_c.detach().cpu().numpy()
-            lower_val = np.percentile(img_c_np, perc[0])
-            upper_val = np.percentile(img_c_np, perc[1])
+            # Percentiles in torch to avoid numpy roundtrip
+            q = torch.tensor([perc[0] / 100.0, perc[1] / 100.0], device=img_c.device, dtype=torch.float32)
+            lower_val, upper_val = torch.quantile(img_c.float(), q)
 
-            img_c_clipped = img_c.clamp(min=float(lower_val), max=float(upper_val))
+            img_c_clipped = img_c.clamp(min=lower_val.item(), max=upper_val.item())
 
             if retain_std[c]:
                 clipped_std = img_c_clipped.std()
@@ -99,4 +98,4 @@ if __name__ == '__main__':
     params = transform.get_parameters(image=image)
     image_clipped = transform._apply_to_image(image.clone(), **params)
 
-    view_batch(image, image_clipped, image_clipped-image)
+    view_batch(image, image_clipped, image_clipped-image)

{batchgeneratorsv2-0.3.0 → batchgeneratorsv2-0.3.3}/batchgeneratorsv2/transforms/nnunet/random_binary_operator.py

@@ -3,14 +3,11 @@ from typing import Union, List, Tuple, Callable
 
 import numpy as np
 import torch
-from fft_conv_pytorch import fft_conv
+from skimage.morphology import ball, disk
 
+from batchgeneratorsv2.helpers.fft_conv import fft_conv
 from batchgeneratorsv2.helpers.scalar_type import RandomScalar, sample_scalar
 from batchgeneratorsv2.transforms.base.basic_transform import ImageOnlyTransform
-from skimage.morphology import ball, disk
-from skimage.morphology.binary import binary_erosion, binary_dilation, binary_closing, binary_opening
-
-import torch.nn.functional as F
 
 
 def binary_dilation_torch(input_tensor, structure_element):

{batchgeneratorsv2-0.3.0 → batchgeneratorsv2-0.3.3}/batchgeneratorsv2/transforms/noise/blank_rectangle.py

@@ -71,7 +71,7 @@ class BlankRectangleTransform(ImageOnlyTransform):
         }
 
     def _apply_to_image(self, img: torch.Tensor, **params) -> torch.Tensor:
-        out = img.clone()
+        out = img
         for c, (apply, rects) in enumerate(zip(params['apply_channel'], params['rectangles'])):
             if not apply:
                 continue
@@ -147,4 +147,4 @@ if __name__ == '__main__':
     image_aug = transform._apply_to_image(image, **params)
 
     from batchviewer import view_batch
-    view_batch(image, image_aug)
+    view_batch(image, image_aug)

{batchgeneratorsv2-0.3.0 → batchgeneratorsv2-0.3.3}/batchgeneratorsv2/transforms/noise/gaussian_blur.py

@@ -6,9 +6,9 @@ import torch
 from skimage.data import camera
 from torch.nn.functional import pad, conv3d, conv1d, conv2d
 
+from batchgeneratorsv2.helpers.fft_conv import fft_conv
 from batchgeneratorsv2.helpers.scalar_type import RandomScalar, sample_scalar
 from batchgeneratorsv2.transforms.base.basic_transform import ImageOnlyTransform
-from fft_conv_pytorch import fft_conv
 
 
 def blur_dimension(img: torch.Tensor, sigma: float, dim_to_blur: int, force_use_fft: bool = None, truncate: float = 6):
@@ -219,7 +219,7 @@ if __name__ == "__main__":
     shape = (128, 164, 64)
     num_warmup_for_benchmark = 1
     num_repeats = 10
-    for sigma_range in (0.1, 1, 10):
+    for sigma_range in (0.1, 1, 10, 20):
         print(shape, sigma_range)
         gnt2 = GaussianBlurTransform(sigma_range, False, False, 1, benchmark=False)
         times = []
@@ -257,4 +257,4 @@ if __name__ == "__main__":
         print('batchgenerator', np.median(times))
         print()
         #
-        # print(gnt.benchmark_use_fft)
+        # print(gnt.benchmark_use_fft)