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# Copyright (c) MONAI Consortium
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from __future__ import annotations
from collections.abc import Callable, Hashable, Mapping
import numpy as np
import torch
from monai.apps.pathology.transforms.post.array import (
GenerateDistanceMap,
GenerateInstanceBorder,
GenerateInstanceCentroid,
GenerateInstanceContour,
GenerateInstanceType,
GenerateSuccinctContour,
GenerateWatershedMarkers,
GenerateWatershedMask,
HoVerNetInstanceMapPostProcessing,
HoVerNetNuclearTypePostProcessing,
Watershed,
)
from monai.config.type_definitions import DtypeLike, KeysCollection, NdarrayOrTensor
from monai.transforms.transform import MapTransform, Transform
from monai.utils import optional_import
from monai.utils.enums import HoVerNetBranch
find_contours, _ = optional_import("skimage.measure", name="find_contours")
__all__ = [
"WatershedD",
"WatershedDict",
"Watershedd",
"GenerateWatershedMaskD",
"GenerateWatershedMaskDict",
"GenerateWatershedMaskd",
"GenerateInstanceBorderD",
"GenerateInstanceBorderDict",
"GenerateInstanceBorderd",
"GenerateDistanceMapD",
"GenerateDistanceMapDict",
"GenerateDistanceMapd",
"GenerateWatershedMarkersD",
"GenerateWatershedMarkersDict",
"GenerateWatershedMarkersd",
"GenerateSuccinctContourDict",
"GenerateSuccinctContourD",
"GenerateSuccinctContourd",
"GenerateInstanceContourDict",
"GenerateInstanceContourD",
"GenerateInstanceContourd",
"GenerateInstanceCentroidDict",
"GenerateInstanceCentroidD",
"GenerateInstanceCentroidd",
"GenerateInstanceTypeDict",
"GenerateInstanceTypeD",
"GenerateInstanceTyped",
"HoVerNetInstanceMapPostProcessingDict",
"HoVerNetInstanceMapPostProcessingD",
"HoVerNetInstanceMapPostProcessingd",
"HoVerNetNuclearTypePostProcessingDict",
"HoVerNetNuclearTypePostProcessingD",
"HoVerNetNuclearTypePostProcessingd",
]
class Watershedd(MapTransform):
"""
Dictionary-based wrapper of :py:class:`monai.apps.pathology.transforms.array.Watershed`.
Use `skimage.segmentation.watershed` to get instance segmentation results from images.
See: https://scikit-image.org/docs/stable/api/skimage.segmentation.html#skimage.segmentation.watershed.
Args:
keys: keys of the corresponding items to be transformed.
See also: monai.transforms.MapTransform
mask_key: keys of mask used in watershed. Only points at which mask == True will be labeled.
markers_key: keys of markers used in watershed. If None (no markers given), the local minima of the image are
used as markers.
connectivity: An array with the same number of dimensions as image whose non-zero elements indicate neighbors
for connection. Following the scipy convention, default is a one-connected array of the dimension of the
image.
dtype: target data content type to convert. Defaults to np.uint8.
allow_missing_keys: don't raise exception if key is missing.
Raises:
ValueError: when the `image` shape is not [1, H, W].
ValueError: when the `mask` shape is not [1, H, W].
"""
backend = Watershed.backend
def __init__(
self,
keys: KeysCollection,
mask_key: str | None = "mask",
markers_key: str | None = None,
connectivity: int | None = 1,
dtype: DtypeLike = np.uint8,
allow_missing_keys: bool = False,
) -> None:
super().__init__(keys, allow_missing_keys)
self.mask_key = mask_key
self.markers_key = markers_key
self.transform = Watershed(connectivity=connectivity, dtype=dtype)
def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]:
d = dict(data)
markers = d[self.markers_key] if self.markers_key else None
mask = d[self.mask_key] if self.mask_key else None
for key in self.key_iterator(d):
d[key] = self.transform(d[key], mask, markers)
return d
class GenerateWatershedMaskd(MapTransform):
"""
Dictionary-based wrapper of :py:class:`monai.apps.pathology.transforms.array.GenerateWatershedMask`.
Args:
keys: keys of the corresponding items to be transformed.
mask_key: the mask will be written to the value of `{mask_key}`.
activation: the activation layer to be applied on nuclear type branch. It can be "softmax" or "sigmoid" string,
or any callable. Defaults to "softmax".
threshold: if not None, threshold the float values to int number 0 or 1 with specified threshold.
min_object_size: objects smaller than this size are removed. Defaults to 10.
dtype: target data content type to convert, default is np.uint8.
allow_missing_keys: don't raise exception if key is missing.
"""
backend = GenerateWatershedMask.backend
def __init__(
self,
keys: KeysCollection,
mask_key: str = "mask",
activation: str | Callable = "softmax",
threshold: float | None = None,
min_object_size: int = 10,
dtype: DtypeLike = np.uint8,
allow_missing_keys: bool = False,
) -> None:
super().__init__(keys, allow_missing_keys)
self.mask_key = mask_key
self.transform = GenerateWatershedMask(
activation=activation, threshold=threshold, min_object_size=min_object_size, dtype=dtype
)
def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]:
d = dict(data)
for key in self.key_iterator(d):
mask = self.transform(d[key])
if self.mask_key in d:
raise KeyError(f"Mask with key {self.mask_key} already exists.")
d[self.mask_key] = mask
return d
class GenerateInstanceBorderd(Transform):
"""
Dictionary-based wrapper of :py:class:`monai.apps.pathology.transforms.array.GenerateInstanceBorder`.
Args:
mask_key: the input key where the watershed mask is stored. Defaults to `"mask"`.
hover_map_key: the input key where hover map is stored. Defaults to `"hover_map"`.
border_key: the output key where instance border map is written. Defaults to `"border"`.
kernel_size: the size of the Sobel kernel. Defaults to 21.
dtype: target data content type to convert, default is np.float32.
allow_missing_keys: don't raise exception if key is missing.
Raises:
ValueError: when the `hover_map` has only one value.
ValueError: when the `sobel gradient map` has only one value.
"""
backend = GenerateInstanceBorder.backend
def __init__(
self,
mask_key: str = "mask",
hover_map_key: str = "hover_map",
border_key: str = "border",
kernel_size: int = 21,
dtype: DtypeLike = np.float32,
) -> None:
self.mask_key = mask_key
self.hover_map_key = hover_map_key
self.border_key = border_key
self.transform = GenerateInstanceBorder(kernel_size=kernel_size, dtype=dtype)
def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]:
d = dict(data)
if self.border_key in d:
raise KeyError(f"The key '{self.border_key}' for instance border map already exists.")
d[self.border_key] = self.transform(d[self.mask_key], d[self.hover_map_key])
return d
class GenerateDistanceMapd(Transform):
"""
Dictionary-based wrapper of :py:class:`monai.apps.pathology.transforms.array.GenerateDistanceMap`.
Args:
mask_key: the input key where the watershed mask is stored. Defaults to `"mask"`.
border_key: the input key where instance border map is stored. Defaults to `"border"`.
dist_map_key: the output key where distance map is written. Defaults to `"dist_map"`.
smooth_fn: smoothing function for distance map, which can be any callable object.
If not provided :py:class:`monai.transforms.GaussianSmooth()` is used.
dtype: target data content type to convert, default is np.float32.
"""
backend = GenerateDistanceMap.backend
def __init__(
self,
mask_key: str = "mask",
border_key: str = "border",
dist_map_key: str = "dist_map",
smooth_fn: Callable | None = None,
dtype: DtypeLike = np.float32,
) -> None:
self.mask_key = mask_key
self.border_key = border_key
self.dist_map_key = dist_map_key
self.transform = GenerateDistanceMap(smooth_fn=smooth_fn, dtype=dtype)
def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]:
d = dict(data)
if self.dist_map_key in d:
raise KeyError(f"The key '{self.dist_map_key}' for distance map already exists.")
d[self.dist_map_key] = self.transform(d[self.mask_key], d[self.border_key])
return d
class GenerateWatershedMarkersd(Transform):
"""
Dictionary-based wrapper of :py:class:`monai.apps.pathology.transforms.array.GenerateWatershedMarkers`.
Args:
mask_key: the input key where the watershed mask is stored. Defaults to `"mask"`.
border_key: the input key where instance border map is stored. Defaults to `"border"`.
markers_key: the output key where markers is written. Defaults to `"markers"`.
threshold: threshold the float values of instance border map to int 0 or 1 with specified threshold.
It turns uncertain area to 1 and other area to 0. Defaults to 0.4.
radius: the radius of the disk-shaped footprint used in `opening`. Defaults to 2.
min_object_size: objects smaller than this size are removed. Defaults to 10.
postprocess_fn: execute additional post transformation on marker. Defaults to None.
dtype: target data content type to convert, default is np.uint8.
allow_missing_keys: don't raise exception if key is missing.
"""
backend = GenerateWatershedMarkers.backend
def __init__(
self,
mask_key: str = "mask",
border_key: str = "border",
markers_key: str = "markers",
threshold: float = 0.4,
radius: int = 2,
min_object_size: int = 10,
postprocess_fn: Callable | None = None,
dtype: DtypeLike = np.uint8,
) -> None:
self.mask_key = mask_key
self.border_key = border_key
self.markers_key = markers_key
self.transform = GenerateWatershedMarkers(
threshold=threshold,
radius=radius,
min_object_size=min_object_size,
postprocess_fn=postprocess_fn,
dtype=dtype,
)
def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]:
d = dict(data)
if self.markers_key in d:
raise KeyError(f"The key '{self.markers_key}' for markers already exists.")
d[self.markers_key] = self.transform(d[self.mask_key], d[self.border_key])
return d
class GenerateSuccinctContourd(MapTransform):
"""
Dictionary-based wrapper of :py:class:`monai.apps.pathology.transforms.post.array.GenerateSuccinctContour`.
Converts SciPy-style contours (generated by skimage.measure.find_contours) to a more succinct version which
only includes the pixels to which lines need to be drawn (i.e. not the intervening pixels along each line).
Args:
keys: keys of the corresponding items to be transformed.
height: height of bounding box, used to detect direction of line segment.
width: width of bounding box, used to detect direction of line segment.
allow_missing_keys: don't raise exception if key is missing.
"""
backend = GenerateSuccinctContour.backend
def __init__(self, keys: KeysCollection, height: int, width: int, allow_missing_keys: bool = False) -> None:
super().__init__(keys, allow_missing_keys)
self.converter = GenerateSuccinctContour(height=height, width=width)
def __call__(self, data):
d = dict(data)
for key in self.key_iterator(d):
d[key] = self.converter(d[key])
return d
class GenerateInstanceContourd(MapTransform):
"""
Dictionary-based wrapper of :py:class:`monai.apps.pathology.transforms.post.array.GenerateInstanceContour`.
Generate contour for each instance in a 2D array. Use `GenerateSuccinctContour` to only include the pixels
to which lines need to be drawn
Args:
keys: keys of the corresponding items to be transformed.
contour_key_postfix: the output contour coordinates will be written to the value of
`{key}_{contour_key_postfix}`.
offset_key: keys of offset used in `GenerateInstanceContour`.
min_num_points: assumed that the created contour does not form a contour if it does not contain more points
than the specified value. Defaults to 3.
level: optional. Value along which to find contours in the array. By default, the level is set
to (max(image) + min(image)) / 2.
allow_missing_keys: don't raise exception if key is missing.
"""
backend = GenerateInstanceContour.backend
def __init__(
self,
keys: KeysCollection,
contour_key_postfix: str = "contour",
offset_key: str | None = None,
min_num_points: int = 3,
level: float | None = None,
allow_missing_keys: bool = False,
) -> None:
super().__init__(keys, allow_missing_keys)
self.converter = GenerateInstanceContour(min_num_points=min_num_points, contour_level=level)
self.contour_key_postfix = contour_key_postfix
self.offset_key = offset_key
def __call__(self, data):
d = dict(data)
for key in self.key_iterator(d):
offset = d[self.offset_key] if self.offset_key else None
contour = self.converter(d[key], offset)
key_to_add = f"{key}_{self.contour_key_postfix}"
if key_to_add in d:
raise KeyError(f"Contour with key {key_to_add} already exists.")
d[key_to_add] = contour
return d
class GenerateInstanceCentroidd(MapTransform):
"""
Dictionary-based wrapper of :py:class:`monai.apps.pathology.transforms.post.array.GenerateInstanceCentroid`.
Generate instance centroid using `skimage.measure.centroid`.
Args:
keys: keys of the corresponding items to be transformed.
centroid_key_postfix: the output centroid coordinates will be written to the value of
`{key}_{centroid_key_postfix}`.
offset_key: keys of offset used in `GenerateInstanceCentroid`.
dtype: the data type of output centroid.
allow_missing_keys: don't raise exception if key is missing.
"""
backend = GenerateInstanceCentroid.backend
def __init__(
self,
keys: KeysCollection,
centroid_key_postfix: str = "centroid",
offset_key: str | None = None,
dtype: DtypeLike | None = int,
allow_missing_keys: bool = False,
) -> None:
super().__init__(keys, allow_missing_keys)
self.converter = GenerateInstanceCentroid(dtype=dtype)
self.centroid_key_postfix = centroid_key_postfix
self.offset_key = offset_key
def __call__(self, data):
d = dict(data)
for key in self.key_iterator(d):
offset = d[self.offset_key] if self.offset_key else None
centroid = self.converter(d[key], offset)
key_to_add = f"{key}_{self.centroid_key_postfix}"
if key_to_add in d:
raise KeyError(f"Centroid with key {key_to_add} already exists.")
d[key_to_add] = centroid
return d
class GenerateInstanceTyped(MapTransform):
"""
Dictionary-based wrapper of :py:class:`monai.apps.pathology.transforms.post.array.GenerateInstanceType`.
Generate instance type and probability for each instance.
Args:
keys: keys of the corresponding items to be transformed.
type_info_key: the output instance type and probability will be written to the value of
`{type_info_key}`.
bbox_key: keys of bounding box.
seg_pred_key: keys of segmentation prediction map.
instance_id_key: keys of instance id.
allow_missing_keys: don't raise exception if key is missing.
"""
backend = GenerateInstanceType.backend
def __init__(
self,
keys: KeysCollection,
type_info_key: str = "type_info",
bbox_key: str = "bbox",
seg_pred_key: str = "seg",
instance_id_key: str = "id",
allow_missing_keys: bool = False,
) -> None:
super().__init__(keys, allow_missing_keys)
self.converter = GenerateInstanceType()
self.type_info_key = type_info_key
self.bbox_key = bbox_key
self.seg_pred_key = seg_pred_key
self.instance_id_key = instance_id_key
def __call__(self, data):
d = dict(data)
for key in self.key_iterator(d):
seg = d[self.seg_pred_key]
bbox = d[self.bbox_key]
id = d[self.instance_id_key]
instance_type, type_prob = self.converter(d[key], seg, bbox, id)
key_to_add = f"{self.type_info_key}"
if key_to_add in d:
raise KeyError(f"Type information with key {key_to_add} already exists.")
d[key_to_add] = {"inst_type": instance_type, "type_prob": type_prob}
return d
class HoVerNetInstanceMapPostProcessingd(Transform):
"""
Dictionary-based wrapper for :py:class:`monai.apps.pathology.transforms.post.array.HoVerNetInstanceMapPostProcessing`.
The post-processing transform for HoVerNet model to generate instance segmentation map.
It generates an instance segmentation map as well as a dictionary containing centroids, bounding boxes, and contours
for each instance.
Args:
nuclear_prediction_key: the key for HoVerNet NP (nuclear prediction) branch. Defaults to `HoVerNetBranch.NP`.
hover_map_key: the key for HoVerNet NC (nuclear prediction) branch. Defaults to `HoVerNetBranch.HV`.
instance_info_key: the output key where instance information (contour, bounding boxes, and centroids)
is written. Defaults to `"instance_info"`.
instance_map_key: the output key where instance map is written. Defaults to `"instance_map"`.
activation: the activation layer to be applied on the input probability map.
It can be "softmax" or "sigmoid" string, or any callable. Defaults to "softmax".
mask_threshold: a float value to threshold to binarize probability map to generate mask.
min_object_size: objects smaller than this size are removed. Defaults to 10.
sobel_kernel_size: the size of the Sobel kernel used in :py:class:`GenerateInstanceBorder`. Defaults to 5.
distance_smooth_fn: smoothing function for distance map.
If not provided, :py:class:`monai.transforms.intensity.GaussianSmooth()` will be used.
marker_threshold: a float value to threshold to binarize instance border map for markers.
It turns uncertain area to 1 and other area to 0. Defaults to 0.4.
marker_radius: the radius of the disk-shaped footprint used in `opening` of markers. Defaults to 2.
marker_postprocess_fn: post-process function for watershed markers.
If not provided, :py:class:`monai.transforms.post.FillHoles()` will be used.
watershed_connectivity: `connectivity` argument of `skimage.segmentation.watershed`.
min_num_points: minimum number of points to be considered as a contour. Defaults to 3.
contour_level: an optional value for `skimage.measure.find_contours` to find contours in the array.
If not provided, the level is set to `(max(image) + min(image)) / 2`.
device: target device to put the output Tensor data.
"""
def __init__(
self,
nuclear_prediction_key: str = HoVerNetBranch.NP.value,
hover_map_key: str = HoVerNetBranch.HV.value,
instance_info_key: str = "instance_info",
instance_map_key: str = "instance_map",
activation: str | Callable = "softmax",
mask_threshold: float | None = None,
min_object_size: int = 10,
sobel_kernel_size: int = 5,
distance_smooth_fn: Callable | None = None,
marker_threshold: float = 0.4,
marker_radius: int = 2,
marker_postprocess_fn: Callable | None = None,
watershed_connectivity: int | None = 1,
min_num_points: int = 3,
contour_level: float | None = None,
device: str | torch.device | None = None,
) -> None:
super().__init__()
self.instance_map_post_process = HoVerNetInstanceMapPostProcessing(
activation=activation,
mask_threshold=mask_threshold,
min_object_size=min_object_size,
sobel_kernel_size=sobel_kernel_size,
distance_smooth_fn=distance_smooth_fn,
marker_threshold=marker_threshold,
marker_radius=marker_radius,
marker_postprocess_fn=marker_postprocess_fn,
watershed_connectivity=watershed_connectivity,
min_num_points=min_num_points,
contour_level=contour_level,
device=device,
)
self.nuclear_prediction_key = nuclear_prediction_key
self.hover_map_key = hover_map_key
self.instance_info_key = instance_info_key
self.instance_map_key = instance_map_key
def __call__(self, data):
d = dict(data)
for k in [self.instance_info_key, self.instance_map_key]:
if k in d:
raise ValueError("The output key ['{k}'] already exists in the input dictionary!")
d[self.instance_info_key], d[self.instance_map_key] = self.instance_map_post_process(
d[self.nuclear_prediction_key], d[self.hover_map_key]
)
return d
class HoVerNetNuclearTypePostProcessingd(Transform):
"""
Dictionary-based wrapper for :py:class:`monai.apps.pathology.transforms.post.array.HoVerNetNuclearTypePostProcessing`.
It updates the input instance info dictionary with information about types of the nuclei (value and probability).
Also if requested (`return_type_map=True`), it generates a pixel-level type map.
Args:
type_prediction_key: the key for HoVerNet NC (type prediction) branch. Defaults to `HoVerNetBranch.NC`.
instance_info_key: the key where instance information (contour, bounding boxes, and centroids) is stored.
Defaults to `"instance_info"`.
instance_map_key: the key where instance map is stored. Defaults to `"instance_map"`.
type_map_key: the output key where type map is written. Defaults to `"type_map"`.
device: target device to put the output Tensor data.
"""
def __init__(
self,
type_prediction_key: str = HoVerNetBranch.NC.value,
instance_info_key: str = "instance_info",
instance_map_key: str = "instance_map",
type_map_key: str = "type_map",
activation: str | Callable = "softmax",
threshold: float | None = None,
return_type_map: bool = True,
device: str | torch.device | None = None,
) -> None:
super().__init__()
self.type_post_process = HoVerNetNuclearTypePostProcessing(
activation=activation, threshold=threshold, return_type_map=return_type_map, device=device
)
self.type_prediction_key = type_prediction_key
self.instance_info_key = instance_info_key
self.instance_map_key = instance_map_key
self.type_map_key = type_map_key
self.return_type_map = return_type_map
def __call__(self, data):
d = dict(data)
d[self.instance_info_key], type_map = self.type_post_process(
d[self.type_prediction_key], d[self.instance_info_key], d[self.instance_map_key]
)
if self.return_type_map:
if self.type_map_key in d:
raise ValueError("The output key ['{self.type_map_key}'] already exists in the input dictionary!")
d[self.type_map_key] = type_map
return d
WatershedD = WatershedDict = Watershedd
GenerateWatershedMaskD = GenerateWatershedMaskDict = GenerateWatershedMaskd
GenerateInstanceBorderD = GenerateInstanceBorderDict = GenerateInstanceBorderd
GenerateDistanceMapD = GenerateDistanceMapDict = GenerateDistanceMapd
GenerateWatershedMarkersD = GenerateWatershedMarkersDict = GenerateWatershedMarkersd
GenerateSuccinctContourDict = GenerateSuccinctContourD = GenerateSuccinctContourd
GenerateInstanceContourDict = GenerateInstanceContourD = GenerateInstanceContourd
GenerateInstanceCentroidDict = GenerateInstanceCentroidD = GenerateInstanceCentroidd
GenerateInstanceTypeDict = GenerateInstanceTypeD = GenerateInstanceTyped
HoVerNetInstanceMapPostProcessingDict = HoVerNetInstanceMapPostProcessingD = HoVerNetInstanceMapPostProcessingd
HoVerNetNuclearTypePostProcessingDict = HoVerNetNuclearTypePostProcessingD = HoVerNetNuclearTypePostProcessingd
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