peak_finding

sleap_nn.inference.peak_finding

Peak finding for inference.

Functions:

Name	Description
crop_bboxes	Crop bounding boxes from a batch of images.
find_global_peaks	Find global peaks with optional refinement.
find_global_peaks_rough	Find the global maximum for each sample and channel.
find_local_peaks	Find local peaks with optional refinement.
find_local_peaks_rough	Find local maxima via non-maximum suppression.
integral_regression	Compute regression by integrating over the confidence maps on a grid.

crop_bboxes(images, bboxes, sample_inds)

Crop bounding boxes from a batch of images.

Parameters:

Name	Type	Description	Default
images	Tensor	Tensor of shape (samples, channels, height, width) of a batch of images.	required
bboxes	Tensor	Tensor of shape (n_bboxes, 4, 2) and dtype torch.float32, where n_bboxes is the number of centroids, and the second dimension represents the four corner points of the bounding boxes, each with x and y coordinates. The order of the corners follows a clockwise arrangement: top-left, top-right, bottom-right, and bottom-left. This can be generated from centroids using make_centered_bboxes.	required
sample_inds	Tensor	Tensor of shape (n_bboxes,) specifying which samples each bounding box should be cropped from.	required

Returns:

Type	Description
Tensor	A tensor of shape (n_bboxes, crop_height, crop_width, channels) of the same dtype as the input image. The crop size is inferred from the bounding box coordinates.

Notes

This function expects bounding boxes with coordinates at the centers of the pixels in the box limits. Technically, the box will span (x1 - 0.5, x2 + 0.5) and (y1 - 0.5, y2 + 0.5).

For example, a 3x3 patch centered at (1, 1) would be specified by (y1, x1, y2, x2) = (0, 0, 2, 2). This would be exactly equivalent to indexing the image with image[:, :, 0:3, 0:3].

See also: make_centered_bboxes

Source code in sleap_nn/inference/peak_finding.py

def crop_bboxes(
    images: torch.Tensor, bboxes: torch.Tensor, sample_inds: torch.Tensor
) -> torch.Tensor:
    """Crop bounding boxes from a batch of images.

    Args:
        images: Tensor of shape (samples, channels, height, width) of a batch of images.
        bboxes: Tensor of shape (n_bboxes, 4, 2) and dtype torch.float32, where n_bboxes
            is the number of centroids, and the second dimension represents the four
            corner points of the bounding boxes, each with x and y coordinates.
            The order of the corners follows a clockwise arrangement: top-left,
            top-right, bottom-right, and bottom-left. This can be generated from
            centroids using `make_centered_bboxes`.
        sample_inds: Tensor of shape (n_bboxes,) specifying which samples each bounding
            box should be cropped from.

    Returns:
        A tensor of shape (n_bboxes, crop_height, crop_width, channels) of the same
        dtype as the input image. The crop size is inferred from the bounding box
        coordinates.

    Notes:
        This function expects bounding boxes with coordinates at the centers of the
        pixels in the box limits. Technically, the box will span (x1 - 0.5, x2 + 0.5)
        and (y1 - 0.5, y2 + 0.5).

        For example, a 3x3 patch centered at (1, 1) would be specified by
        (y1, x1, y2, x2) = (0, 0, 2, 2). This would be exactly equivalent to indexing
        the image with `image[:, :, 0:3, 0:3]`.

    See also: `make_centered_bboxes`
    """
    # Compute bounding box size to use for crops.
    height = abs(bboxes[0, 3, 1] - bboxes[0, 0, 1])
    width = abs(bboxes[0, 1, 0] - bboxes[0, 0, 0])
    box_size = tuple(torch.round(torch.Tensor((height + 1, width + 1))).to(torch.int32))

    # Crop.
    crops = crop_and_resize(
        images[sample_inds],  # (n_boxes, channels, height, width)
        boxes=bboxes,
        size=box_size,
    )

    # Cast back to original dtype and return.
    crops = crops.to(images.dtype)
    return crops

find_global_peaks(cms, threshold=0.2, refinement=None, integral_patch_size=5)

Find global peaks with optional refinement.

Parameters:

Name	Type	Description	Default
cms	Tensor	Confidence maps. Tensor of shape (samples, channels, height, width).	required
threshold	float	Minimum confidence threshold. Peaks with values below this will ignored.	0.2
refinement	Optional[str]	If None, returns the grid-aligned peaks with no refinement. If "integral", peaks will be refined with integral regression.	None
integral_patch_size	int	Size of patches to crop around each rough peak as an integer scalar.	5

Returns:

Type	Description
Tuple[Tensor, Tensor]	A tuple of (peak_points, peak_vals). peak_points: float32 tensor of shape (samples, channels, 2), where the last axis indicates peak locations in xy order. peak_vals: float32 tensor of shape (samples, channels) containing the values at the peak points.

Source code in sleap_nn/inference/peak_finding.py

def find_global_peaks(
    cms: torch.Tensor,
    threshold: float = 0.2,
    refinement: Optional[str] = None,
    integral_patch_size: int = 5,
) -> Tuple[torch.Tensor, torch.Tensor]:
    """Find global peaks with optional refinement.

    Args:
        cms: Confidence maps. Tensor of shape (samples, channels, height, width).
        threshold: Minimum confidence threshold. Peaks with values below this will
            ignored.
        refinement: If `None`, returns the grid-aligned peaks with no refinement. If
            `"integral"`, peaks will be refined with integral regression.
        integral_patch_size: Size of patches to crop around each rough peak as an
            integer scalar.

    Returns:
        A tuple of (peak_points, peak_vals).

        peak_points: float32 tensor of shape (samples, channels, 2), where the last axis
        indicates peak locations in xy order.

        peak_vals: float32 tensor of shape (samples, channels) containing the values at
        the peak points.
    """
    # Find grid aligned peaks.
    rough_peaks, peak_vals = find_global_peaks_rough(
        cms, threshold=threshold
    )  # (samples, channels, 2)

    # Return early if not refining or no rough peaks found.
    if refinement is None or torch.isnan(rough_peaks).all():
        return rough_peaks, peak_vals

    if refinement == "integral":
        crop_size = integral_patch_size
    else:
        return rough_peaks, peak_vals

    # Flatten samples and channels to (n_peaks, 2).
    samples = cms.size(0)
    channels = cms.size(1)
    rough_peaks = rough_peaks.view(samples * channels, 2)

    # Keep only peaks that are not NaNs.
    valid_idx = torch.where(~torch.isnan(rough_peaks[:, 0]))[0]
    valid_peaks = rough_peaks[valid_idx]

    # Make bounding boxes for cropping around peaks.
    bboxes = make_centered_bboxes(
        valid_peaks, box_height=crop_size, box_width=crop_size
    )

    # Crop patch around each grid-aligned peak.
    cms = torch.reshape(
        cms,
        [samples * channels, 1, cms.size(2), cms.size(3)],
    )
    cm_crops = crop_bboxes(cms, bboxes, valid_idx)

    # Compute offsets via integral regression on a local patch.
    if refinement == "integral":
        gv = torch.arange(crop_size, dtype=torch.float32) - ((crop_size - 1) / 2)
        dx_hat, dy_hat = integral_regression(cm_crops, xv=gv, yv=gv)
        offsets = torch.cat([dx_hat, dy_hat], dim=1)

    # Apply offsets.
    refined_peaks = rough_peaks.clone()
    refined_peaks[valid_idx] += offsets

    # Reshape to (samples, channels, 2).
    refined_peaks = refined_peaks.reshape(samples, channels, 2)

    return refined_peaks, peak_vals

find_global_peaks_rough(cms, threshold=0.1)

Find the global maximum for each sample and channel.

Parameters:

Name	Type	Description	Default
cms	Tensor	Tensor of shape (samples, channels, height, width).	required
threshold	float	Scalar float specifying the minimum confidence value for peaks. Peaks with values below this threshold will be replaced with NaNs.	0.1

Returns:

Type	Description
Tuple[Tensor, Tensor]	A tuple of (peak_points, peak_vals). peak_points: float32 tensor of shape (samples, channels, 2), where the last axis indicates peak locations in xy order. peak_vals: float32 tensor of shape (samples, channels) containing the values at the peak points.

Source code in sleap_nn/inference/peak_finding.py

def find_global_peaks_rough(
    cms: torch.Tensor, threshold: float = 0.1
) -> Tuple[torch.Tensor, torch.Tensor]:
    """Find the global maximum for each sample and channel.

    Args:
        cms: Tensor of shape (samples, channels, height, width).
        threshold: Scalar float specifying the minimum confidence value for peaks. Peaks
            with values below this threshold will be replaced with NaNs.

    Returns:
        A tuple of (peak_points, peak_vals).
        peak_points: float32 tensor of shape (samples, channels, 2), where the last axis
        indicates peak locations in xy order.
        peak_vals: float32 tensor of shape (samples, channels) containing the values at
        the peak points.

    """
    # Find the maximum values and their indices along the height and width axes.
    max_values, max_indices_y = torch.max(cms, dim=2, keepdim=True)
    max_values, max_indices_x = torch.max(max_values, dim=3, keepdim=True)
    max_indices_x = max_indices_x.squeeze(dim=(2, 3))  # (samples, channels)
    # Find the maximum values and their indices along the height and width axes.
    amax_values, amax_indices_x = torch.max(cms, dim=3, keepdim=True)
    amax_values, amax_indices_y = torch.max(amax_values, dim=2, keepdim=True)
    amax_indices_y = amax_indices_y.squeeze(dim=(2, 3))
    peak_points = torch.cat(
        [max_indices_x.unsqueeze(-1), amax_indices_y.unsqueeze(-1)], dim=-1
    ).to(torch.float32)
    max_values = max_values.squeeze(-1).squeeze(-1)
    # Create masks for values below the threshold.
    below_threshold_mask = max_values < threshold
    # Replace values below the threshold with NaN.
    peak_points[below_threshold_mask] = float("nan")
    max_values[below_threshold_mask] = float(0)
    return peak_points, max_values

find_local_peaks(cms, threshold=0.2, refinement=None, integral_patch_size=5)

Find local peaks with optional refinement.

Parameters:

Name	Type	Description	Default
cms	Tensor	Confidence maps. Tensor of shape (samples, channels, height, width).	required
threshold	float	Minimum confidence threshold. Peaks with values below this will ignored.	0.2
refinement	Optional[str]	If None, returns the grid-aligned peaks with no refinement. If "integral", peaks will be refined with integral regression.	None
integral_patch_size	int	Size of patches to crop around each rough peak as an integer scalar.	5

Returns:

Type

Description

Tuple[Tensor, Tensor, Tensor, Tensor]

A tuple of (peak_points, peak_vals, peak_sample_inds, peak_channel_inds). peak_points: float32 tensor of shape (n_peaks, 2), where the last axis indicates peak locations in xy order. peak_vals: float32 tensor of shape (n_peaks,) containing the values at the peak points. peak_sample_inds: int32 tensor of shape (n_peaks,) containing the indices of the sample each peak belongs to. peak_channel_inds: int32 tensor of shape (n_peaks,) containing the indices of the channel each peak belongs to.

Source code in sleap_nn/inference/peak_finding.py

def find_local_peaks(
    cms: torch.Tensor,
    threshold: float = 0.2,
    refinement: Optional[str] = None,
    integral_patch_size: int = 5,
) -> Tuple[torch.Tensor, torch.Tensor, torch.Tensor, torch.Tensor]:
    """Find local peaks with optional refinement.

    Args:
        cms: Confidence maps. Tensor of shape (samples, channels, height, width).
        threshold: Minimum confidence threshold. Peaks with values below this will
            ignored.
        refinement: If `None`, returns the grid-aligned peaks with no refinement. If
            `"integral"`, peaks will be refined with integral regression.
        integral_patch_size: Size of patches to crop around each rough peak as an
            integer scalar.

    Returns:
        A tuple of (peak_points, peak_vals, peak_sample_inds, peak_channel_inds).

        peak_points: float32 tensor of shape (n_peaks, 2), where the last axis
        indicates peak locations in xy order.

        peak_vals: float32 tensor of shape (n_peaks,) containing the values at the peak
        points.

        peak_sample_inds: int32 tensor of shape (n_peaks,) containing the indices of the
        sample each peak belongs to.

        peak_channel_inds: int32 tensor of shape (n_peaks,) containing the indices of
        the channel each peak belongs to.
    """
    # Find grid aligned peaks.
    (
        rough_peaks,
        peak_vals,
        peak_sample_inds,
        peak_channel_inds,
    ) = find_local_peaks_rough(cms, threshold=threshold)

    # Return early if no rough peaks found.
    if rough_peaks.size(0) == 0 or refinement is None:
        return rough_peaks, peak_vals, peak_sample_inds, peak_channel_inds

    if refinement == "integral":
        crop_size = integral_patch_size
    else:
        return rough_peaks, peak_vals, peak_sample_inds, peak_channel_inds

    # Make bounding boxes for cropping around peaks.
    bboxes = make_centered_bboxes(
        rough_peaks, box_height=crop_size, box_width=crop_size
    )

    # Reshape to (samples * channels, height, width, 1).
    samples = cms.size(0)
    channels = cms.size(1)
    cms = torch.reshape(
        cms,
        [samples * channels, 1, cms.size(2), cms.size(3)],
    )
    box_sample_inds = (peak_sample_inds * channels) + peak_channel_inds

    # Crop patch around each grid-aligned peak.
    cm_crops = crop_bboxes(cms, bboxes, sample_inds=box_sample_inds)

    # Compute offsets via integral regression on a local patch.
    if refinement == "integral":
        gv = torch.arange(crop_size, dtype=torch.float32) - ((crop_size - 1) / 2)
        dx_hat, dy_hat = integral_regression(cm_crops, xv=gv, yv=gv)
        offsets = torch.cat([dx_hat, dy_hat], dim=1)

    # Apply offsets.
    refined_peaks = rough_peaks + offsets

    return refined_peaks, peak_vals, peak_sample_inds, peak_channel_inds

find_local_peaks_rough(cms, threshold=0.2)

Find local maxima via non-maximum suppression.

Parameters:

Name	Type	Description	Default
cms	Tensor	Tensor of shape (samples, channels, height, width).	required
threshold	float	Scalar float specifying the minimum confidence value for peaks. Peaks with values below this threshold will not be returned.	0.2

Returns:

Type

Description

Tuple[Tensor, Tensor, Tensor, Tensor]

A tuple of (peak_points, peak_vals, peak_sample_inds, peak_channel_inds). peak_points: float32 tensor of shape (n_peaks, 2), where the last axis indicates peak locations in xy order. peak_vals: float32 tensor of shape (n_peaks,) containing the values at the peak points. peak_sample_inds: int32 tensor of shape (n_peaks,) containing the indices of the sample each peak belongs to. peak_channel_inds: int32 tensor of shape (n_peaks,) containing the indices of the channel each peak belongs to.

Source code in sleap_nn/inference/peak_finding.py

def find_local_peaks_rough(
    cms: torch.Tensor, threshold: float = 0.2
) -> Tuple[torch.Tensor, torch.Tensor, torch.Tensor, torch.Tensor]:
    """Find local maxima via non-maximum suppression.

    Args:
        cms: Tensor of shape (samples, channels, height, width).
        threshold: Scalar float specifying the minimum confidence value for peaks. Peaks
            with values below this threshold will not be returned.

    Returns:
        A tuple of (peak_points, peak_vals, peak_sample_inds, peak_channel_inds).
        peak_points: float32 tensor of shape (n_peaks, 2), where the last axis
        indicates peak locations in xy order.

        peak_vals: float32 tensor of shape (n_peaks,) containing the values at the peak
        points.

        peak_sample_inds: int32 tensor of shape (n_peaks,) containing the indices of the
        sample each peak belongs to.

        peak_channel_inds: int32 tensor of shape (n_peaks,) containing the indices of
        the channel each peak belongs to.
    """
    # Build custom local NMS kernel.
    kernel = torch.tensor([[1, 1, 1], [1, 0, 1], [1, 1, 1]], dtype=torch.float32)

    # Reshape to have singleton channels.
    height = cms.size(2)
    width = cms.size(3)
    channels = cms.size(1)
    flat_img = cms.reshape(-1, 1, height, width)

    # Perform dilation filtering to find local maxima per channel and reshape back.
    max_img = K.morphology.dilation(flat_img, kernel.to(flat_img.device))
    max_img = max_img.reshape(-1, channels, height, width)

    # Filter for maxima and threshold.
    argmax_and_thresh_img = (cms > max_img) & (cms > threshold)

    # Convert to subscripts.
    peak_subs = torch.stack(
        torch.where(argmax_and_thresh_img.permute(0, 2, 3, 1)), axis=-1
    )

    # Get peak values.
    peak_vals = cms[peak_subs[:, 0], peak_subs[:, 3], peak_subs[:, 1], peak_subs[:, 2]]

    # Convert to points format.
    peak_points = peak_subs[:, [2, 1]].to(torch.float32)

    # Pull out indexing vectors.
    peak_sample_inds = peak_subs[:, 0].to(torch.int32)
    peak_channel_inds = peak_subs[:, 3].to(torch.int32)

    return peak_points, peak_vals, peak_sample_inds, peak_channel_inds

integral_regression(cms, xv, yv)

Compute regression by integrating over the confidence maps on a grid.

Parameters:

Name	Type	Description	Default
cms	Tensor	Confidence maps with shape (samples, channels, height, width).	required
xv	Tensor	X grid vector torch.float32 of grid coordinates to sample.	required
yv	Tensor	Y grid vector torch.float32 of grid coordinates to sample.	required

Returns:

Type	Description
Tuple[Tensor, Tensor]	A tuple of (x_hat, y_hat) with the regressed x- and y-coordinates for each channel of the confidence maps. x_hat and y_hat are of shape (samples, channels)

Source code in sleap_nn/inference/peak_finding.py

def integral_regression(
    cms: torch.Tensor, xv: torch.Tensor, yv: torch.Tensor
) -> Tuple[torch.Tensor, torch.Tensor]:
    """Compute regression by integrating over the confidence maps on a grid.

    Args:
        cms: Confidence maps with shape (samples, channels, height, width).
        xv: X grid vector torch.float32 of grid coordinates to sample.
        yv: Y grid vector torch.float32 of grid coordinates to sample.

    Returns:
        A tuple of (x_hat, y_hat) with the regressed x- and y-coordinates for each
        channel of the confidence maps.

        x_hat and y_hat are of shape (samples, channels)
    """
    # Compute normalizing factor.
    z = torch.sum(cms, dim=[2, 3]).to(cms.device)
    xv = xv.to(cms.device)
    yv = yv.to(cms.device)

    # Regress to expectation.
    x_hat = torch.sum(xv.view(1, 1, 1, -1) * cms, dim=[2, 3]) / z
    y_hat = torch.sum(yv.view(1, 1, -1, 1) * cms, dim=[2, 3]) / z

    return x_hat, y_hat