On the fly rescaling (GPU)

src/membrain_seg/segmentation/cli/cli.py

@@ -18,6 +18,7 @@ def list_commands(self, ctx: Context):
     add_completion=False,
     no_args_is_help=True,
     rich_markup_mode="rich",
+    pretty_exceptions_show_locals=False
 )
 OPTION_PROMPT_KWARGS = {"prompt": True, "prompt_required": True}
 PKWARGS = OPTION_PROMPT_KWARGS

src/membrain_seg/segmentation/cli/segment_cli.py

@@ -27,6 +27,19 @@ def segment(
     out_folder: str = Option(  # noqa: B008
         "./predictions", help="Path to the folder where segmentations should be stored."
     ),
+    rescale_patches: bool = Option( # noqa: B008
+        False, help="Should patches be rescaled on-the-fly during inference?"
+    ),
+    in_pixel_size: float = Option(  # noqa: B008
+        None,
+        help="Pixel size of the input tomogram in Angstrom. \
+            (default: 10 Angstrom)",
+    ),
+    out_pixel_size: float = Option(  # noqa: B008
+        10.,
+        help="Pixel size of the output segmentation in Angstrom. \
+            (default: 10 Angstrom; should normally stay at 10 Angstrom)",
+    ),
     store_probabilities: bool = Option(  # noqa: B008
         False, help="Should probability maps be output in addition to segmentations?"
     ),
@@ -66,6 +79,9 @@ def segment(
         tomogram_path=tomogram_path,
         ckpt_path=ckpt_path,
         out_folder=out_folder,
+        rescale_patches=rescale_patches,
+        in_pixel_size=in_pixel_size,
+        out_pixel_size=out_pixel_size,
         store_probabilities=store_probabilities,
         store_connected_components=store_connected_components,
         connected_component_thres=connected_component_thres,

src/membrain_seg/segmentation/networks/inference_unet.py

@@ -0,0 +1,105 @@
+from typing import Tuple
+
+import torch
+import torch.nn.functional as F
+
+from membrain_seg.segmentation.networks.unet import SemanticSegmentationUnet
+from membrain_seg.tomo_preprocessing.matching_utils.px_matching_utils import (
+    fourier_cropping_torch,
+    fourier_extend_torch,
+)
+
+
+def rescale_tensor(
+    sample: torch.Tensor, target_size: tuple, mode="trilinear"
+) -> torch.Tensor:
+    """
+    Rescales the input tensor by given factors using interpolation.
+
+    Parameters
+    ----------
+    sample : torch.Tensor
+        The input data as a torch tensor.
+    target_size : tuple
+        The target size of the rescaled tensor.
+    mode : str, optional
+        The mode of interpolation ('nearest', 'linear', 'bilinear',
+          'bicubic', or 'trilinear'). Default is 'trilinear'.
+
+    Returns
+    -------
+    torch.Tensor
+        The rescaled tensor.
+    """
+    # Add batch and channel dimensions
+    sample = sample.unsqueeze(0).unsqueeze(0)
+
+    # Apply interpolation
+    rescaled_sample = F.interpolate(
+        sample, size=target_size, mode=mode, align_corners=False
+    )
+
+    return rescaled_sample.squeeze(0).squeeze(0)
+
+
+class PreprocessedSemanticSegmentationUnet(SemanticSegmentationUnet):
+    """U-Net with rescaling preprocessing.
+
+    This class extends the SemanticSegmentationUnet class by adding
+    preprocessing and postprocessing steps. The preprocessing step
+    rescales the input to the target shape, and the postprocessing
+    step rescales the output to the original shape.
+    All of this is done on the GPU if available.
+    """
+
+    def __init__(
+        self,
+        *args,
+        rescale_patches: bool = False,  # Should patches be rescaled?
+        target_shape: Tuple[int, int, int] = (160, 160, 160),
+        **kwargs,
+    ):
+        super().__init__(*args, **kwargs)
+        # Store the preprocessing parameters
+        self.rescale_patches = rescale_patches
+        self.target_shape = target_shape
+
+    def preprocess(self, x):
+        """Preprocess the input to the network.
+
+        In this case, we rescale the input to the target shape.
+        """
+        rescaled_samples = []
+        for sample in x:
+            sample = sample[0]  # only use the first channel
+            if self.rescale_patches:
+                if sample.shape[0] > self.target_shape[0]:
+                    sample = fourier_cropping_torch(sample, self.target_shape)
+                elif sample.shape[0] < self.target_shape[0]:
+                    sample = fourier_extend_torch(sample, self.target_shape)
+            rescaled_samples.append(sample.unsqueeze(0))
+        rescaled_samples = torch.stack(rescaled_samples, dim=0)
+        return rescaled_samples
+
+    def postprocess(self, x, orig_shape):
+        """Postprocess the output of the network.
+
+        In this case, we rescale the output to the original shape.
+        """
+        rescaled_samples = []
+        for sample in x:
+            sample = sample[0]  # only use first channel
+            if self.rescale_patches:
+                sample = rescale_tensor(sample, orig_shape, mode="trilinear")
+            rescaled_samples.append(sample.unsqueeze(0))
+        rescaled_samples = torch.stack(rescaled_samples, dim=0)
+        return rescaled_samples
+
+    def forward(self, x):
+        """Forward pass through the network."""
+        orig_shape = x.shape[2:]
+        preprocessed_x = self.preprocess(x)
+        predicted = super().forward(preprocessed_x)
+        postprocessed_predicted = self.postprocess(predicted[0], orig_shape)
+        # Return list to be compatible with deep supervision outputs
+        return [postprocessed_predicted]

src/membrain_seg/segmentation/segment.py

@@ -3,7 +3,12 @@
 import torch
 from monai.inferers import SlidingWindowInferer
 
-from membrain_seg.segmentation.networks.unet import SemanticSegmentationUnet
+from membrain_seg.segmentation.networks.inference_unet import (
+    PreprocessedSemanticSegmentationUnet,
+)
+from membrain_seg.tomo_preprocessing.matching_utils.px_matching_utils import (
+    determine_output_shape,
+)
 
 from .dataloading.data_utils import (
     load_data_for_inference,
@@ -16,6 +21,9 @@ def segment(
     tomogram_path,
     ckpt_path,
     out_folder,
+    rescale_patches=False,
+    in_pixel_size=None,
+    out_pixel_size=10.0,
     store_probabilities=False,
     sw_roi_size=160,
     store_connected_components=False,
@@ -40,6 +48,12 @@ def segment(
         Path to the trained model checkpoint file.
     out_folder : str
         Path to the folder where the output segmentations should be stored.
+    rescale_patches : bool, optional
+        If True, rescale the patches to the output pixel size (default is False).
+    in_pixel_size : float, optional
+        Pixel size of the input tomogram in Angstrom (default is None).
+    out_pixel_size : float, optional
+        Pixel size of the output segmentation in Angstrom (default is 10.0).
     store_probabilities : bool, optional
         If True, store the predicted probabilities along with the segmentations
         (default is False).
@@ -78,10 +92,13 @@ def segment(
     device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
 
     # Initialize the model and load trained weights from checkpoint
-    pl_model = SemanticSegmentationUnet.load_from_checkpoint(
+    pl_model = PreprocessedSemanticSegmentationUnet.load_from_checkpoint(
         model_checkpoint, map_location=device, strict=False
     )
     pl_model.to(device)
+    if sw_roi_size % 32 != 0:
+        raise OSError("Sliding window size must be multiple of 32°!")
+    pl_model.target_shape = (sw_roi_size, sw_roi_size, sw_roi_size)
 
     # Preprocess the new data
     new_data_path = tomogram_path
@@ -91,12 +108,34 @@ def segment(
     )
     new_data = new_data.to(torch.float32)
 
+    if rescale_patches:
+        # Rescale patches if necessary
+        if in_pixel_size is None:
+            in_pixel_size = voxel_size.x
+        if in_pixel_size == 0.0:
+            raise ValueError(
+                "Input pixel size is 0.0. Please specify the pixel size manually."
+            )
+        if in_pixel_size == 1.0:
+            print(
+                "WARNING: Input pixel size is 1.0. Looks like a corrupt header.",
+                "Please specify the pixel size manually.",
+            )
+        pl_model.rescale_patches = in_pixel_size != out_pixel_size
+
+        # Determine the sliding window size according to the input and output pixel size
+        sw_roi_size = determine_output_shape(
+            # switch in and out pixel size to get SW shape
+            pixel_size_in=out_pixel_size,
+            pixel_size_out=in_pixel_size,
+            orig_shape=(sw_roi_size, sw_roi_size, sw_roi_size),
+        )
+        sw_roi_size = sw_roi_size[0]
+
     # Put the model into evaluation mode
     pl_model.eval()
 
     # Perform sliding window inference on the new data
-    if sw_roi_size % 32 != 0:
-        raise OSError("Sliding window size must be multiple of 32°!")
     roi_size = (sw_roi_size, sw_roi_size, sw_roi_size)
     sw_batch_size = 1
     inferer = SlidingWindowInferer(
@@ -110,20 +149,20 @@ def segment(
 
     # Perform test time augmentation (8-fold mirroring)
     predictions = torch.zeros_like(new_data)
-    print("Performing 8-fold test-time augmentation.")
+    if test_time_augmentation:
+        print(
+            "Performing 8-fold test-time augmentation.",
+            "I.e. the following bar will run 8 times.",
+        )
     for m in range(8 if test_time_augmentation else 1):
         with torch.no_grad():
             with torch.cuda.amp.autocast():
-                predictions += (
-                    get_mirrored_img(
-                        inferer(
-                            get_mirrored_img(new_data.clone(), m).to(device), pl_model
-                        )[0],
-                        m,
-                    )
-                    .detach()
-                    .cpu()
-                )
+                mirrored_input = get_mirrored_img(new_data.clone(), m).to(device)
+                mirrored_pred = inferer(mirrored_input, pl_model)
+                if not isinstance(mirrored_pred, list):
+                    mirrored_pred = [mirrored_pred]
+                correct_pred = get_mirrored_img(mirrored_pred[0], m)
+                predictions += correct_pred.detach().cpu()
     if test_time_augmentation:
         predictions /= 8.0
 

src/membrain_seg/tomo_preprocessing/matching_utils/px_matching_utils.py

@@ -1,10 +1,95 @@
 from typing import Tuple, Union
 
 import numpy as np
+import torch
+import torch.fft
 from scipy.fft import fftn, ifftn
 from scipy.ndimage import distance_transform_edt
 
 
+def fourier_cropping_torch(data: torch.Tensor, new_shape: tuple) -> torch.Tensor:
+    """
+    Fourier cropping adapted for PyTorch and GPU, without smoothing functionality.
+
+    Parameters
+    ----------
+    data : torch.Tensor
+        The input data as a 3D torch tensor on GPU.
+    new_shape : tuple
+        The target shape for the cropped data as a tuple (x, y, z).
+
+    Returns
+    -------
+    torch.Tensor
+        The resized data as a 3D torch tensor.
+    """
+    device = "cuda" if torch.cuda.is_available() else "cpu"
+    data = data.to(device)
+
+    # Calculate the FFT of the input data
+    data_fft = torch.fft.fftn(data)
+    data_fft = torch.fft.fftshift(data_fft)
+
+    # Calculate the cropping indices
+    original_shape = torch.tensor(data.shape, device=device)
+    new_shape = torch.tensor(new_shape, device=device)
+    start_indices = (original_shape - new_shape) // 2
+    end_indices = start_indices + new_shape
+
+    # Crop the filtered FFT data
+    cropped_fft = data_fft[
+        start_indices[0] : end_indices[0],
+        start_indices[1] : end_indices[1],
+        start_indices[2] : end_indices[2],
+    ]
+
+    unshifted_cropped_fft = torch.fft.ifftshift(cropped_fft)
+
+    # Calculate the inverse FFT of the cropped data
+    resized_data = torch.real(torch.fft.ifftn(unshifted_cropped_fft))
+
+    return resized_data
+
+
+def fourier_extend_torch(data: torch.Tensor, new_shape: tuple) -> torch.Tensor:
+    """
+    Fourier padding adapted for PyTorch and GPU, without smoothing functionality.
+
+    Parameters
+    ----------
+    data : torch.Tensor
+        The input data as a 3D torch tensor on GPU.
+    new_shape : tuple
+        The target shape for the extended data as a tuple (x, y, z).
+
+    Returns
+    -------
+    torch.Tensor
+        The resized data as a 3D torch tensor.
+    """
+    device = "cuda" if torch.cuda.is_available() else "cpu"
+    data = data.to(device)
+
+    data_fft = torch.fft.fftn(data)
+    data_fft = torch.fft.fftshift(data_fft)
+
+    padding = [
+        (new_dim - old_dim) // 2 for old_dim, new_dim in zip(data.shape, new_shape)
+    ]
+    padded_fft = torch.nn.functional.pad(
+        data_fft,
+        pad=[pad for pair in zip(padding, padding) for pad in pair],
+        mode="constant",
+    )
+
+    unshifted_padded_fft = torch.fft.ifftshift(padded_fft)
+
+    # Calculate the inverse FFT of the cropped data
+    resized_data = torch.real(torch.fft.ifftn(unshifted_padded_fft))
+
+    return resized_data
+
+
 def smooth_cosine_dropoff(mask: np.ndarray, decay_width: float) -> np.ndarray:
     """
     Apply a smooth cosine drop-off to a given mask.