from warnings import warn
import numpy as np
from .base import Image
[docs]class BooleanImage(Image):
r"""
A mask image made from binary pixels. The region of the image that is
left exposed by the mask is referred to as the 'masked region'. The
set of 'masked' pixels is those pixels corresponding to a ``True`` value in
the mask.
Parameters
----------
mask_data : ``(M, N, ..., L)`` `ndarray`
The binary mask data. Note that there is no channel axis - a 2D Mask
Image is built from just a 2D numpy array of mask_data.
Automatically coerced in to boolean values.
copy: `bool`, optional
If ``False``, the image_data will not be copied on assignment. Note that
if the array you provide is not boolean, there **will still be copy**.
In general this should only be used if you know what you are doing.
"""
def __init__(self, mask_data, copy=True):
# Add a channel dimension. We do this little reshape trick to add
# the axis because this maintains C-contiguous'ness
mask_data = mask_data.reshape(mask_data.shape + (1,))
# If we are trying not to copy, but the data we have isn't boolean,
# then unfortunately, we forced to copy anyway!
if mask_data.dtype != np.bool:
mask_data = np.array(mask_data, dtype=np.bool, copy=True,
order='C')
if not copy:
warn('The copy flag was NOT honoured. A copy HAS been made. '
'Please ensure the data you pass is C-contiguous.')
super(BooleanImage, self).__init__(mask_data, copy=copy)
[docs] def as_masked(self, mask=None, copy=True):
r"""
Impossible for a :map:`BooleanImage` to be transformed to a
:map:`MaskedImage`.
"""
raise NotImplementedError("as_masked cannot be invoked on a "
"BooleanImage.")
@classmethod
[docs] def blank(cls, shape, fill=True, round='ceil', **kwargs):
r"""
Returns a blank :map:`BooleanImage` of the requested shape
Parameters
----------
shape : `tuple` or `list`
The shape of the image. Any floating point values are rounded
according to the ``round`` kwarg.
fill : `bool`, optional
The mask value to be set everywhere.
round: ``{ceil, floor, round}``, optional
Rounding function to be applied to floating point shapes.
Returns
-------
blank_image : :map:`BooleanImage`
A blank mask of the requested size
"""
from .base import round_image_shape
shape = round_image_shape(shape, round)
if fill:
mask = np.ones(shape, dtype=np.bool)
else:
mask = np.zeros(shape, dtype=np.bool)
return cls(mask, copy=False)
@property
def mask(self):
r"""
Returns the pixels of the mask with no channel axis. This is what
should be used to mask any k-dimensional image.
:type: ``(M, N, ..., L)``, `bool ndarray`
"""
return self.pixels[..., 0]
[docs] def n_true(self):
r"""
The number of ``True`` values in the mask.
:type: `int`
"""
return np.sum(self.pixels)
[docs] def n_false(self):
r"""
The number of ``False`` values in the mask.
:type: `int`
"""
return self.n_pixels - self.n_true()
[docs] def all_true(self):
r"""
``True`` iff every element of the mask is ``True``.
:type: `bool`
"""
return np.all(self.pixels)
[docs] def proportion_true(self):
r"""
The proportion of the mask which is ``True``.
:type: `float`
"""
return (self.n_true() * 1.0) / self.n_pixels
[docs] def proportion_false(self):
r"""
The proportion of the mask which is ``False``
:type: `float`
"""
return (self.n_false() * 1.0) / self.n_pixels
[docs] def true_indices(self):
r"""
The indices of pixels that are ``True``.
:type: ``(n_dims, n_true)`` `ndarray`
"""
if self.all_true():
return self.indices()
else:
# Ignore the channel axis
return np.vstack(np.nonzero(self.pixels[..., 0])).T
[docs] def false_indices(self):
r"""
The indices of pixels that are ``Flase``.
:type: ``(n_dims, n_false)`` `ndarray`
"""
# Ignore the channel axis
return np.vstack(np.nonzero(~self.pixels[..., 0])).T
def __str__(self):
return ('{} {}D mask, {:.1%} '
'of which is True'.format(self._str_shape, self.n_dims,
self.proportion_true()))
[docs] def from_vector(self, vector, copy=True):
r"""
Takes a flattened vector and returns a new :map:`BooleanImage` formed
by reshaping the vector to the correct dimensions. Note that this is
rebuilding a boolean image **itself** from boolean values. The mask
is in no way interpreted in performing the operation, in contrast to
:map:`MaskedImage`, where only the masked region is used in
:meth:`from_vector` and :meth`as_vector`. Any image landmarks are
transferred in the process.
Parameters
----------
vector : ``(n_pixels,)`` `bool ndarray`
A flattened vector of all the pixels of a :map:`BooleanImage`.
copy : `bool`, optional
If ``False``, no copy of the vector will be taken.
Returns
-------
image : :map:`BooleanImage`
New BooleanImage of same shape as this image
Raises
------
Warning
If ``copy=False`` cannot be honored.
"""
mask = BooleanImage(vector.reshape(self.shape), copy=copy)
mask.landmarks = self.landmarks
return mask
[docs] def invert_inplace(self):
r"""
Inverts this Boolean Image inplace.
"""
self.pixels = ~self.pixels
[docs] def invert(self):
r"""
Returns a copy of this boolean image, which is inverted.
Returns
-------
inverted : :map:`BooleanImage`
A copy of this boolean mask, where all ``True`` values are ``False``
and all ``False`` values are ``True``.
"""
inverse = self.copy()
inverse.invert_inplace()
return inverse
[docs] def bounds_true(self, boundary=0, constrain_to_bounds=True):
r"""
Returns the minimum to maximum indices along all dimensions that the
mask includes which fully surround the ``True`` mask values. In the case
of a 2D Image for instance, the min and max define two corners of a
rectangle bounding the True pixel values.
Parameters
----------
boundary : `int`, optional
A number of pixels that should be added to the extent. A
negative value can be used to shrink the bounds in.
constrain_to_bounds: `bool`, optional
If ``True``, the bounding extent is snapped to not go beyond
the edge of the image. If ``False``, the bounds are left unchanged.
Returns
--------
min_b : ``(D,)`` `ndarray`
The minimum extent of the ``True`` mask region with the boundary
along each dimension. If ``constrain_to_bounds=True``,
is clipped to legal image bounds.
max_b : ``(D,)`` `ndarray`
The maximum extent of the ``True`` mask region with the boundary
along each dimension. If ``constrain_to_bounds=True``,
is clipped to legal image bounds.
"""
mpi = self.true_indices()
maxes = np.max(mpi, axis=0) + boundary
mins = np.min(mpi, axis=0) - boundary
if constrain_to_bounds:
maxes = self.constrain_points_to_bounds(maxes)
mins = self.constrain_points_to_bounds(mins)
return mins, maxes
[docs] def bounds_false(self, boundary=0, constrain_to_bounds=True):
r"""
Returns the minimum to maximum indices along all dimensions that the
mask includes which fully surround the False mask values. In the case
of a 2D Image for instance, the min and max define two corners of a
rectangle bounding the False pixel values.
Parameters
----------
boundary : `int` >= 0, optional
A number of pixels that should be added to the extent. A
negative value can be used to shrink the bounds in.
constrain_to_bounds: `bool`, optional
If ``True``, the bounding extent is snapped to not go beyond
the edge of the image. If ``False``, the bounds are left unchanged.
Returns
-------
min_b : ``(D,)`` `ndarray`
The minimum extent of the ``True`` mask region with the boundary
along each dimension. If ``constrain_to_bounds=True``,
is clipped to legal image bounds.
max_b : ``(D,)`` `ndarray`
The maximum extent of the ``True`` mask region with the boundary
along each dimension. If ``constrain_to_bounds=True``,
is clipped to legal image bounds.
"""
return self.invert().bounds_true(
boundary=boundary, constrain_to_bounds=constrain_to_bounds)
# noinspection PyMethodOverriding
[docs] def warp_to_mask(self, template_mask, transform, warp_landmarks=True,
mode='constant', cval=0.):
r"""
Return a copy of this :map:`BooleanImage` warped into a different
reference space.
Note that warping into a mask is slower than warping into a full image.
If you don't need a non-linear mask, consider warp_to_shape instead.
Parameters
----------
template_mask : :map:`BooleanImage`
Defines the shape of the result, and what pixels should be
sampled.
transform : :map:`Transform`
Transform **from the template space back to this image**.
Defines, for each pixel location on the template, which pixel
location should be sampled from on this image.
warp_landmarks : `bool`, optional
If ``True``, result will have the same landmark dictionary
as self, but with each landmark updated to the warped position.
mode : ``{constant, nearest, reflect or wrap}``, optional
Points outside the boundaries of the input are filled according
to the given mode.
cval : `float`, optional
Used in conjunction with mode ``constant``, the value outside
the image boundaries.
Returns
-------
warped_image : :map:`BooleanImage`
A copy of this image, warped.
"""
# enforce the order as 0, for this boolean data, then call super
return Image.warp_to_mask(self, template_mask, transform,
warp_landmarks=warp_landmarks,
order=0, mode=mode, cval=cval)
# noinspection PyMethodOverriding
[docs] def warp_to_shape(self, template_shape, transform, warp_landmarks=True,
mode='constant', cval=0., order=None):
"""
Return a copy of this :map:`BooleanImage` warped into a different
reference space.
Note that the order keyword argument is in fact ignored, as any order
other than 0 makes no sense on a binary image. The keyword argument is
present only for compatibility with the :map:`Image` warp_to_shape API.
Parameters
----------
template_shape : ``(n_dims, )`` `tuple` or `ndarray`
Defines the shape of the result, and what pixel indices should be
sampled (all of them).
transform : :map:`Transform`
Transform **from the template_shape space back to this image**.
Defines, for each index on template_shape, which pixel location
should be sampled from on this image.
warp_landmarks : `bool`, optional
If ``True``, result will have the same landmark dictionary
as self, but with each landmark updated to the warped position.
mode : ``{constant, nearest, reflect or wrap}``, optional
Points outside the boundaries of the input are filled according
to the given mode.
cval : `float`, optional
Used in conjunction with mode ``constant``, the value outside
the image boundaries.
Returns
-------
warped_image : :map:`BooleanImage`
A copy of this image, warped.
"""
# call the super variant and get ourselves an Image back
# note that we force the use of order=0 for BooleanImages.
warped = Image.warp_to_shape(self, template_shape, transform,
warp_landmarks=warp_landmarks,
order=0, mode=mode, cval=cval)
# unfortunately we can't escape copying here, let BooleanImage
# convert us to np.bool
boolean_image = BooleanImage(warped.pixels.reshape(template_shape))
if warped.has_landmarks:
boolean_image.landmarks = warped.landmarks
if hasattr(warped, 'path'):
boolean_image.path = warped.path
return boolean_image
def _build_warped_to_mask(self, template_mask, sampled_pixel_values,
**kwargs):
r"""
Builds the warped image from the template mask and sampled pixel values.
"""
# start from a copy of the template_mask
warped_img = template_mask.copy()
if warped_img.all_true():
# great, just reshape the sampled_pixel_values
warped_img.pixels = sampled_pixel_values.reshape(
warped_img.shape + (1,))
else:
# we have to fill out mask with the sampled mask..
warped_img.pixels[warped_img.mask] = sampled_pixel_values
return warped_img
[docs] def constrain_to_landmarks(self, group=None, label=None, trilist=None):
r"""
Restricts this mask to be equal to the convex hull around the
landmarks chosen. This is not a per-pixel convex hull, but instead
relies on a triangulated approximation.
Parameters
----------
group : `str`, optional
The key of the landmark set that should be used. If ``None``,
and if there is only one set of landmarks, this set will be used.
label: `str`, optional
The label of of the landmark manager that you wish to use. If no
label is passed, the convex hull of all landmarks is used.
trilist: ``(t, 3)`` `ndarray`, optional
Triangle list to be used on the landmarked points in selecting
the mask region. If ``None``, defaults to performing Delaunay
triangulation on the points.
"""
self.constrain_to_pointcloud(self.landmarks[group][label],
trilist=trilist)
[docs] def constrain_to_pointcloud(self, pointcloud, trilist=None):
r"""
Restricts this mask to be equal to the convex hull around a point cloud.
This is not a per-pixel convex hull, but instead
relies on a triangulated approximation.
Parameters
----------
pointcloud : :map:`PointCloud`
The pointcloud of points that should be constrained to.
trilist: ``(t, 3)`` `ndarray`, optional
Triangle list to be used on the landmarked points in selecting
the mask region. If None defaults to performing Delaunay
triangulation on the points.
"""
from menpo.transform.piecewiseaffine import PiecewiseAffine
from menpo.transform.piecewiseaffine import TriangleContainmentError
if self.n_dims != 2:
raise ValueError("can only constrain mask on 2D images.")
if trilist is not None:
from menpo.shape import TriMesh
pointcloud = TriMesh(pointcloud.points, trilist)
pwa = PiecewiseAffine(pointcloud, pointcloud)
try:
pwa.apply(self.indices())
except TriangleContainmentError as e:
self.from_vector_inplace(~e.points_outside_source_domain)