Erase features in 3D from 3D mask

src/fidder/erase/cli.py

@@ -7,6 +7,7 @@
 from typer import Option
 
 from .erase import erase_masked_region as _erase_masked_region
+from .erase import erase_masked_region_3d as _erase_masked_region_3d
 from ..utils import get_pixel_spacing_from_header
 from .._cli import cli, OPTION_PROMPT_KWARGS as PKWARGS
 
@@ -54,3 +55,43 @@ def erase_masked_region(
         voxel_size=pixel_spacing,
         overwrite=True,
     )
+
+
+@cli.command(name="erase_3d", no_args_is_help=True)
+def erase_masked_region_3d(
+    input_image: Path = Option(
+        default=...,
+        help="Image file in MRC format.",
+        **PKWARGS
+    ),
+    input_mask: Path = Option(
+        default=...,
+        help="Mask file in MRC format.",
+        **PKWARGS
+    ),
+    output_image: Path = Option(
+        default=...,
+        help="Output file in MRC format.",
+        **PKWARGS
+    ),
+):
+    """Erase a masked region in a cryo-EM image."""
+    volume = torch.as_tensor(mrcfile.read(input_image)).squeeze().float()
+    mask = torch.as_tensor(mrcfile.read(input_mask), dtype=torch.bool).squeeze()
+    if volume.shape != mask.shape:
+        raise ValueError('Shape mismatch between data in volume and mask files.')
+
+    erased_volume = _erase_masked_region_3d(
+        volume=volume,
+        mask=mask,
+        background_intensity_model_resolution=(8, 8, 8),
+        background_intensity_model_samples=25000,
+    )
+
+    pixel_spacing = get_pixel_spacing_from_header(input_image)
+    mrcfile.write(
+        name=output_image,
+        data=np.array(erased_volume, dtype=np.float32),
+        voxel_size=pixel_spacing,
+        overwrite=True,
+    )

src/fidder/erase/erase.py

@@ -4,8 +4,8 @@
 import torch
 from einops import einops
 
-from ..utils import estimate_background_std
-from .sparse_local_mean import estimate_local_mean
+from ..utils import estimate_background_std, estimate_background_std_3d
+from .sparse_local_mean import estimate_local_mean, estimate_local_mean_3d
 
 
 def erase_masked_region(
@@ -108,3 +108,60 @@ def _erase_single_image(
                              size=n_pixels_to_inpaint)
     inpainted_image[idx_foreground] += torch.as_tensor(noise)
     return inpainted_image
+
+
+def erase_masked_region_3d(
+    volume: torch.Tensor,
+    mask: torch.Tensor,
+    background_intensity_model_resolution: Tuple[int, int, int] = (5, 5, 5),
+    background_intensity_model_samples: int = 20000,
+) -> torch.Tensor:
+    """Inpaint image(s) with gaussian noise.
+
+
+    Parameters
+    ----------
+    image: torch.Tensor
+        `(b, h, w)` or `(h, w)` array containing image data for erase.
+    mask: torch.Tensor
+        `(b, h, w)` or `(h, w)` binary mask separating foreground from background pixels.
+        Foreground pixels (1) will be inpainted.
+    background_intensity_model_resolution: Tuple[int, int]
+        Number of points in each image dimension for the background mean model.
+        Minimum of two points in each dimension.
+    background_intensity_model_samples: int
+        Number of sample points used to determine the model of the background mean.
+
+    Returns
+    -------
+    inpainted_image: torch.Tensor
+        `(b, h, w)` or `(h, w)` array containing image data inpainted in the foreground pixels of the mask
+        with gaussian noise matching the local mean and global standard deviation of the image
+        for background pixels.
+    """
+    volume = torch.as_tensor(volume)
+    mask = torch.as_tensor(mask, dtype=torch.bool)
+    if volume.shape != mask.shape:
+        raise ValueError("image shape must match mask shape.")
+
+    inpainted = torch.clone(volume)
+    local_mean = estimate_local_mean_3d(
+        volume=volume,
+        mask=torch.logical_not(mask),
+        resolution=background_intensity_model_resolution,
+        n_samples_for_fit=background_intensity_model_samples,
+    )
+
+    # fill foreground pixels with local mean
+    idx_foreground = torch.argwhere(mask.bool() == True)
+    idx_foreground = (idx_foreground[:, 0], idx_foreground[:, 1], idx_foreground[:, 2])
+
+    inpainted[idx_foreground] = local_mean[idx_foreground]
+
+    # add noise with mean=0 std=background std estimate
+    background_std = estimate_background_std_3d(volume, mask)
+    n_pixels_to_inpaint = idx_foreground[0].shape[0]
+    noise = np.random.normal(loc=0, scale=background_std, size=(n_pixels_to_inpaint, 3))
+    inpainted[idx_foreground] += torch.as_tensor(np.mean(noise, axis=1))
+
+    return torch.as_tensor(inpainted, dtype=torch.float32)

src/fidder/erase/sparse_local_mean.py

@@ -3,6 +3,7 @@
 import numpy as np
 import torch
 from scipy.interpolate import LSQBivariateSpline
+from torch_cubic_spline_grids.b_spline_grids import CubicBSplineGrid3d
 
 
 def estimate_local_mean(
@@ -59,3 +60,71 @@ def estimate_local_mean(
     x = np.arange(image.shape[-1])
     local_mean = background_model(y, x, grid=True)
     return torch.tensor(local_mean, dtype=input_dtype)
+
+
+def estimate_local_mean_3d(
+    volume: torch.Tensor,
+    mask: Optional[torch.Tensor] = None,
+    resolution: Tuple[int, int, int] = (5, 5, 5),
+    n_samples_for_fit: int = 20000,
+):
+    """Estimate local mean of an image with a bivariate cubic spline.
+
+    A mask can be provided to
+
+    Parameters
+    ----------
+    image: torch.Tensor
+        `(h, w)` array containing image data.
+    mask: Optional[torch.Tensor]
+        `(h, w)` array containing a binary mask specifying foreground
+        and background pixels for the estimation.
+    resolution: Tuple[int, int]
+        Resolution of the local mean estimate in each dimension.
+    n_samples_for_fit: int
+        Number of samples taken from foreground pixels for background mean estimation.
+        The number of background pixels will be used if this number is greater than the
+        number of background pixels.
+
+    Returns
+    -------
+    local_mean: torch.Tensor
+        `(h, w)` array containing a local estimate of the local mean.
+    """
+    input_dtype = volume.dtype
+    volume = volume.numpy()
+    mask = np.ones_like(volume) if mask is None else mask.numpy()
+
+    # get a random set of foreground pixels for the background fit
+    foreground_sample_idx = np.argwhere(mask == 1)
+
+    n_samples_for_fit = min(n_samples_for_fit, len(foreground_sample_idx))
+    selection = np.random.choice(
+        foreground_sample_idx.shape[0], size=n_samples_for_fit, replace=False
+    )
+    foreground_sample_idx = foreground_sample_idx[selection]
+    z, y, x = foreground_sample_idx[:, 0], foreground_sample_idx[:, 1], foreground_sample_idx[:, 2]
+
+    w = torch.as_tensor(volume[(z, y, x)])
+
+    grid = CubicBSplineGrid3d(resolution=resolution)
+    optimiser = torch.optim.Adam(grid.parameters(), lr=0.01)
+
+    for i in range(500):
+        # what does the model predict for our observations?
+        prediction = grid(foreground_sample_idx).squeeze()
+
+        # zero gradients and calculate loss between observations and model prediction
+        optimiser.zero_grad()
+        loss = torch.sum((prediction - w)**2)**0.5
+
+        # backpropagate loss and update values at points on grid
+        loss.backward()
+        optimiser.step()
+
+    tz = torch.tensor(np.linspace(0, 1, volume.shape[0]))
+    ty = torch.tensor(np.linspace(0, 1, volume.shape[1]))
+    tx = torch.tensor(np.linspace(0, 1, volume.shape[2]))
+    zz, yy, xx = torch.meshgrid(tz, ty, tx, indexing='xy')
+    w = grid(torch.stack((zz, yy, xx), dim=-1)).detach().numpy().reshape(volume.shape)
+    return torch.tensor(w, dtype=input_dtype)

src/fidder/utils.py

@@ -101,6 +101,28 @@ def central_crop_2d(image: torch.Tensor, percentage: float = 25) -> torch.Tensor
     return image[..., hf:hc, wf:wc]
 
 
+def central_crop_3d(image: torch.Tensor, percentage: float = 25) -> torch.Tensor:
+    """Get a central crop of (a batch of) 2D image(s).
+
+    Parameters
+    ----------
+    image: torch.Tensor
+        `(b, h, w)` or `(h, w)` array of 2D images.
+    percentage: float
+        percentage of image height and width for cropped region.
+    Returns
+    -------
+    cropped_image: torch.Tensor
+        `(b, h, w)` or `(h, w)` array of cropped 2D images.
+    """
+    h, w, d = image.shape[-3], image.shape[-2], image.shape[-1]
+    mh, mw, md = h // 2, w // 2, d // 2
+    dh, dw, dd = int(h * (percentage / 100 / 2)), int(w * (percentage / 100 / 2)), int(d * (percentage / 100 / 2))
+    hf, wf, df = mh - dh, mw - dw, md - dd
+    hc, wc, dc = mh + dh, mw + dw, md + dd
+    return image[..., hf:hc, wf:wc, df:dc]
+
+
 def estimate_background_std(image: torch.Tensor, mask: torch.Tensor):
     """Estimate the standard deviation of the background from a central crop.
 
@@ -120,6 +142,31 @@ def estimate_background_std(image: torch.Tensor, mask: torch.Tensor):
     return torch.std(image[mask == 0])
 
 
+def estimate_background_std_3d(image: torch.Tensor, mask: torch.Tensor):
+    """Estimate the standard deviation of the background from a central crop.
+
+    Parameters
+    ----------
+    image: torch.Tensor
+        `(h, w)` array containing data for which background standard deviation will be estimated.
+    mask: torch.Tensor of 0 or 1
+        Binary mask separating foreground and background.
+    Returns
+    -------
+    standard_deviation: float
+        estimated standard deviation for the background.
+    """
+    image = central_crop_3d(image, percentage=25).float()
+    mask = central_crop_3d(mask, percentage=25)
+    image_masked = image.clone()
+    image_masked[mask == 1] = np.nan
+    return (
+        np.nanmean(np.nanstd(image_masked, axis=0)),
+        np.nanmean(np.nanstd(image_masked, axis=1)),
+        np.nanmean(np.nanstd(image_masked, axis=2)),
+    )
+
+
 def get_pixel_spacing_from_header(image: Path) -> float:
     with mrcfile.open(image, header_only=True, permissive=True) as mrc:
         return float(mrc.voxel_size.x)