def plot_2d_or_3d_image(
data: Union[torch.Tensor, np.ndarray],
step: int,
writer,
index: int = 0,
max_channels: int = 1,
max_frames: int = 64,
tag: str = "output",
):
"""Plot 2D or 3D image on the TensorBoard, 3D image will be converted to GIF image.
Note:
Plot 3D or 2D image(with more than 3 channels) as separate images.
Args:
data (Tensor or np.array): target data to be plotted as image on the TensorBoard.
The data is expected to have 'NCHW[D]' dimensions, and only plot the first in the batch.
step: current step to plot in a chart.
writer (SummaryWriter): specify TensorBoard SummaryWriter to plot the image.
index: plot which element in the input data batch, default is the first element.
max_channels: number of channels to plot.
max_frames: number of frames for 2D-t plot.
tag: tag of the plotted image on TensorBoard.
"""
assert isinstance(writer, SummaryWriter) is True, "must provide a TensorBoard SummaryWriter."
d = data[index]
if torch.is_tensor(d):
d = d.detach().cpu().numpy()
if d.ndim == 2:
d = rescale_array(d, 0, 1)
dataformats = "HW"
writer.add_image(f"{tag}_{dataformats}", d, step, dataformats=dataformats)
return
if d.ndim == 3:
if d.shape[0] == 3 and max_channels == 3: # RGB
dataformats = "CHW"
writer.add_image(f"{tag}_{dataformats}", d, step, dataformats=dataformats)
return
for j, d2 in enumerate(d[:max_channels]):
d2 = rescale_array(d2, 0, 1)
dataformats = "HW"
writer.add_image(f"{tag}_{dataformats}_{j}", d2, step, dataformats=dataformats)
return
if d.ndim >= 4:
spatial = d.shape[-3:]
for j, d3 in enumerate(d.reshape([-1] + list(spatial))[:max_channels]):
d3 = rescale_array(d3, 0, 255)
add_animated_gif(writer, f"{tag}_HWD_{j}", d3[None], max_frames, 1.0, step)
return
def create_test_image_3d(
height: int,
width: int,
depth: int,
num_objs: int = 12,
rad_max: int = 30,
noise_max: float = 0.0,
num_seg_classes: int = 5,
channel_dim: Optional[int] = None,
random_state: Optional[np.random.RandomState] = None,
) -> Tuple[np.ndarray, np.ndarray]:
"""
Return a noisy 3D image and segmentation.
Args:
height: height of the image.
width: width of the image.
depth: depth of the image.
num_objs: number of circles to generate. Defaults to `12`.
rad_max: maximum circle radius. Defaults to `30`.
noise_max: if greater than 0 then noise will be added to the image taken from
the uniform distribution on range `[0,noise_max)`. Defaults to `0`.
num_seg_classes: number of classes for segmentations. Defaults to `5`.
channel_dim: if None, create an image without channel dimension, otherwise create
an image with channel dimension as first dim or last dim. Defaults to `None`.
random_state: the random generator to use. Defaults to `np.random`.
See also:
:py:meth:`~create_test_image_2d`
"""
image = np.zeros((width, height, depth))
rs = np.random if random_state is None else random_state
for _ in range(num_objs):
x = rs.randint(rad_max, width - rad_max)
y = rs.randint(rad_max, height - rad_max)
z = rs.randint(rad_max, depth - rad_max)
rad = rs.randint(5, rad_max)
spy, spx, spz = np.ogrid[-x:width - x, -y:height - y, -z:depth - z]
circle = (spx * spx + spy * spy + spz * spz) <= rad * rad
if num_seg_classes > 1:
image[circle] = np.ceil(rs.random() * num_seg_classes)
else:
image[circle] = rs.random() * 0.5 + 0.5
labels = np.ceil(image).astype(np.int32)
norm = rs.uniform(0, num_seg_classes * noise_max, size=image.shape)
noisyimage = rescale_array(np.maximum(image, norm))
if channel_dim is not None:
assert isinstance(
channel_dim,
int) and channel_dim in (-1, 0, 3), "invalid channel dim."
noisyimage, labels = ((noisyimage[None],
labels[None]) if channel_dim == 0 else
(noisyimage[..., None], labels[..., None]))
return noisyimage, labels
def create_test_image_3d(height,
width,
depth,
num_objs=12,
rad_max=30,
noise_max=0.0,
num_seg_classes=5):
"""
Return a noisy 3D image and segmentation.
See also: create_test_image_2d
"""
image = np.zeros((width, height, depth))
for i in range(num_objs):
x = np.random.randint(rad_max, width - rad_max)
y = np.random.randint(rad_max, height - rad_max)
z = np.random.randint(rad_max, depth - rad_max)
rad = np.random.randint(5, rad_max)
spy, spx, spz = np.ogrid[-x:width - x, -y:height - y, -z:depth - z]
circle = (spx * spx + spy * spy + spz * spz) <= rad * rad
if num_seg_classes > 1:
image[circle] = np.ceil(np.random.random() * num_seg_classes)
else:
image[circle] = np.random.random() * 0.5 + 0.5
labels = np.ceil(image).astype(np.int32)
norm = np.random.uniform(0, num_seg_classes * noise_max, size=image.shape)
noisyimage = rescale_array(np.maximum(image, norm))
return noisyimage, labels
def create_test_image_2d(width,
height,
num_objs=12,
rad_max=30,
noise_max=0.0,
num_seg_classes=5):
"""
Return a noisy 2D image with `numObj' circles and a 2D mask image. The maximum radius of the circles is given as
`radMax'. The mask will have `numSegClasses' number of classes for segmentations labeled sequentially from 1, plus a
background class represented as 0. If `noiseMax' is greater than 0 then noise will be added to the image taken from
the uniform distribution on range [0,noiseMax).
"""
image = np.zeros((width, height))
for i in range(num_objs):
x = np.random.randint(rad_max, width - rad_max)
y = np.random.randint(rad_max, height - rad_max)
rad = np.random.randint(5, rad_max)
spy, spx = np.ogrid[-x:width - x, -y:height - y]
circle = (spx * spx + spy * spy) <= rad * rad
if num_seg_classes > 1:
image[circle] = np.ceil(np.random.random() * num_seg_classes)
else:
image[circle] = np.random.random() * 0.5 + 0.5
labels = np.ceil(image).astype(np.int32)
norm = np.random.uniform(0, num_seg_classes * noise_max, size=image.shape)
noisyimage = rescale_array(np.maximum(image, norm))
return noisyimage, labels
def create_test_image_2d(
width: int,
height: int,
num_objs: int = 12,
rad_max: int = 30,
noise_max: float = 0.0,
num_seg_classes: int = 5,
channel_dim: Optional[int] = None,
random_state: Optional[np.random.RandomState] = None,
) -> Tuple[np.ndarray, np.ndarray]:
"""
Return a noisy 2D image with `num_objs` circles and a 2D mask image. The maximum radius of the circles is given as
`rad_max`. The mask will have `num_seg_classes` number of classes for segmentations labeled sequentially from 1, plus a
background class represented as 0. If `noise_max` is greater than 0 then noise will be added to the image taken from
the uniform distribution on range `[0,noise_max)`. If `channel_dim` is None, will create an image without channel
dimension, otherwise create an image with channel dimension as first dim or last dim.
Args:
width: width of the image.
height: height of the image.
num_objs: number of circles to generate. Defaults to `12`.
rad_max: maximum circle radius. Defaults to `30`.
noise_max: if greater than 0 then noise will be added to the image taken from
the uniform distribution on range `[0,noise_max)`. Defaults to `0`.
num_seg_classes: number of classes for segmentations. Defaults to `5`.
channel_dim: if None, create an image without channel dimension, otherwise create
an image with channel dimension as first dim or last dim. Defaults to `None`.
random_state: the random generator to use. Defaults to `np.random`.
"""
image = np.zeros((width, height))
rs = np.random if random_state is None else random_state
for _ in range(num_objs):
x = rs.randint(rad_max, width - rad_max)
y = rs.randint(rad_max, height - rad_max)
rad = rs.randint(5, rad_max)
spy, spx = np.ogrid[-x : width - x, -y : height - y]
circle = (spx * spx + spy * spy) <= rad * rad
if num_seg_classes > 1:
image[circle] = np.ceil(rs.random() * num_seg_classes)
else:
image[circle] = rs.random() * 0.5 + 0.5
labels = np.ceil(image).astype(np.int32)
norm = rs.uniform(0, num_seg_classes * noise_max, size=image.shape)
noisyimage = rescale_array(np.maximum(image, norm))
if channel_dim is not None:
if not (isinstance(channel_dim, int) and channel_dim in (-1, 0, 2)):
raise AssertionError("invalid channel dim.")
if channel_dim == 0:
noisyimage = noisyimage[None]
labels = labels[None]
else:
noisyimage = noisyimage[..., None]
labels = labels[..., None]
return noisyimage, labels
def __call__(self, img):
"""
Apply the transform to `img`.
"""
if self.minv is not None and self.maxv is not None:
return rescale_array(img, self.minv, self.maxv, img.dtype)
else:
return (img * (1 + self.factor)).astype(img.dtype)
def blend_images(image: NdarrayOrTensor,
label: NdarrayOrTensor,
alpha: float = 0.5,
cmap: str = "hsv",
rescale_arrays: bool = True):
"""
Blend an image and a label. Both should have the shape CHW[D].
The image may have C==1 or 3 channels (greyscale or RGB).
The label is expected to have C==1.
Args:
image: the input image to blend with label data.
label: the input label to blend with image data.
alpha: when blending image and label, `alpha` is the weight for the image region mapping to `label != 0`,
and `1 - alpha` is the weight for the label region that `label != 0`, default to `0.5`.
cmap: specify colormap in the matplotlib, default to `hsv`, for more details, please refer to:
https://matplotlib.org/2.0.2/users/colormaps.html.
rescale_arrays: whether to rescale the array to [0, 1] first, default to `True`.
"""
if label.shape[0] != 1:
raise ValueError("Label should have 1 channel")
if image.shape[0] not in (1, 3):
raise ValueError("Image should have 1 or 3 channels")
# rescale arrays to [0, 1] if desired
if rescale_arrays:
image = rescale_array(image)
label = rescale_array(label)
# convert image to rgb (if necessary) and then rgba
if image.shape[0] == 1:
image = repeat(image, 3, axis=0)
def get_label_rgb(cmap: str, label: NdarrayOrTensor):
_cmap = cm.get_cmap(cmap)
label_np, *_ = convert_data_type(label, np.ndarray)
label_rgb_np = _cmap(label_np[0])
label_rgb_np = np.moveaxis(label_rgb_np, -1, 0)[:3]
label_rgb, *_ = convert_to_dst_type(label_rgb_np, label)
return label_rgb
label_rgb = get_label_rgb(cmap, label)
w_image = where(label == 0, 1.0, alpha)
w_label = where(label == 0, 0.0, 1 - alpha)
return w_image * image + w_label * label_rgb
def test_max_none(self):
for p in TEST_NDARRAYS:
scaler = ScaleIntensity(minv=0.0, maxv=None, factor=0.1)
result = scaler(p(self.imt))
expected = rescale_array(p(self.imt), minv=0.0, maxv=None)
assert_allclose(result,
expected,
type_test="tensor",
rtol=1e-3,
atol=1e-3)
def _add_2_or_3_d(self, data, step, tag='output'):
# for i, d in enumerate(data): # go through a batch of images
d = data[0] # show the first element in a batch
if d.ndim == 2:
d = rescale_array(d, 0, 1)
dataformats = 'HW'
self._writer.add_image('{}_{}'.format(tag, dataformats),
d,
step,
dataformats=dataformats)
return
if d.ndim == 3:
if d.shape[0] == 3 and self.max_channels == 3: # RGB
dataformats = 'CHW'
self._writer.add_image('{}_{}'.format(tag, dataformats),
d,
step,
dataformats=dataformats)
return
for j, d2 in enumerate(d[:self.max_channels]):
d2 = rescale_array(d2, 0, 1)
dataformats = 'HW'
self._writer.add_image('{}_{}_{}'.format(tag, dataformats, j),
d2,
step,
dataformats=dataformats)
return
if d.ndim >= 4:
spatial = d.shape[-3:]
for j, d3 in enumerate(
d.reshape([-1] + list(spatial))[:self.max_channels]):
d3 = rescale_array(d3, 0, 255)
img2tensorboard.add_animated_gif(self._writer,
'{}_HWD_{}'.format(tag, j),
d3[None], self.max_frames,
1.0, step)
return
def __call__(self, img: np.ndarray) -> np.ndarray:
"""
Apply the transform to `img`.
Raises:
ValueError: When ``self.minv=None`` or ``self.maxv=None`` and ``self.factor=None``. Incompatible values.
"""
if self.minv is not None and self.maxv is not None:
return rescale_array(img, self.minv, self.maxv, img.dtype)
if self.factor is not None:
return (img * (1 + self.factor)).astype(img.dtype)
raise ValueError("Incompatible values: minv=None or maxv=None and factor=None.")
def create_test_image_3d(
height: int,
width: int,
depth: int,
num_objs: int = 12,
rad_max: int = 30,
noise_max: float = 0.0,
num_seg_classes: int = 5,
channel_dim: Optional[int] = None,
random_state: Optional[np.random.RandomState] = None,
):
"""
Return a noisy 3D image and segmentation.
See also:
:py:meth:`~create_test_image_2d`
"""
image = np.zeros((width, height, depth))
rs = np.random if random_state is None else random_state
for _ in range(num_objs):
x = rs.randint(rad_max, width - rad_max)
y = rs.randint(rad_max, height - rad_max)
z = rs.randint(rad_max, depth - rad_max)
rad = rs.randint(5, rad_max)
spy, spx, spz = np.ogrid[-x:width - x, -y:height - y, -z:depth - z]
circle = (spx * spx + spy * spy + spz * spz) <= rad * rad
if num_seg_classes > 1:
image[circle] = np.ceil(rs.random() * num_seg_classes)
else:
image[circle] = rs.random() * 0.5 + 0.5
labels = np.ceil(image).astype(np.int32)
norm = rs.uniform(0, num_seg_classes * noise_max, size=image.shape)
noisyimage = rescale_array(np.maximum(image, norm))
if channel_dim is not None:
assert isinstance(
channel_dim,
int) and channel_dim in (-1, 0, 3), "invalid channel dim."
noisyimage, labels = ((noisyimage[None],
labels[None]) if channel_dim == 0 else
(noisyimage[..., None], labels[..., None]))
return noisyimage, labels
def create_test_image_2d(width,
height,
num_objs=12,
rad_max=30,
noise_max=0.0,
num_seg_classes=5,
channel_dim=None):
"""
Return a noisy 2D image with `num_obj` circles and a 2D mask image. The maximum radius of the circles is given as
`rad_max`. The mask will have `num_seg_classes` number of classes for segmentations labeled sequentially from 1, plus a
background class represented as 0. If `noise_max` is greater than 0 then noise will be added to the image taken from
the uniform distribution on range `[0,noise_max)`. If `channel_dim` is None, will create an image without channel
dimension, otherwise create an image with channel dimension as first dim or last dim.
"""
image = np.zeros((width, height))
for i in range(num_objs):
x = np.random.randint(rad_max, width - rad_max)
y = np.random.randint(rad_max, height - rad_max)
rad = np.random.randint(5, rad_max)
spy, spx = np.ogrid[-x:width - x, -y:height - y]
circle = (spx * spx + spy * spy) <= rad * rad
if num_seg_classes > 1:
image[circle] = np.ceil(np.random.random() * num_seg_classes)
else:
image[circle] = np.random.random() * 0.5 + 0.5
labels = np.ceil(image).astype(np.int32)
norm = np.random.uniform(0, num_seg_classes * noise_max, size=image.shape)
noisyimage = rescale_array(np.maximum(image, norm))
if channel_dim is not None:
assert isinstance(
channel_dim,
int) and channel_dim in (-1, 0, 2), "invalid channel dim."
noisyimage, labels = (
noisyimage[None],
labels[None] if channel_dim == 0 else
(noisyimage[..., None], labels[..., None]),
)
return noisyimage, labels
def create_test_image_3d(height,
width,
depth,
num_objs=12,
rad_max=30,
noise_max=0.0,
num_seg_classes=5,
channel_dim=None):
"""
Return a noisy 3D image and segmentation.
See also:
:py:meth:`~create_test_image_2d`
"""
image = np.zeros((width, height, depth))
for i in range(num_objs):
x = np.random.randint(rad_max, width - rad_max)
y = np.random.randint(rad_max, height - rad_max)
z = np.random.randint(rad_max, depth - rad_max)
rad = np.random.randint(5, rad_max)
spy, spx, spz = np.ogrid[-x:width - x, -y:height - y, -z:depth - z]
circle = (spx * spx + spy * spy + spz * spz) <= rad * rad
if num_seg_classes > 1:
image[circle] = np.ceil(np.random.random() * num_seg_classes)
else:
image[circle] = np.random.random() * 0.5 + 0.5
labels = np.ceil(image).astype(np.int32)
norm = np.random.uniform(0, num_seg_classes * noise_max, size=image.shape)
noisyimage = rescale_array(np.maximum(image, norm))
if channel_dim is not None:
assert isinstance(
channel_dim,
int) and channel_dim in (-1, 0, 3), 'invalid channel dim.'
noisyimage, labels = (noisyimage[None], labels[None]) \
if channel_dim == 0 else (noisyimage[..., None], labels[..., None])
return noisyimage, labels
def __call__(self, img):
if self.minv is not None and self.maxv is not None:
return rescale_array(img, self.minv, self.maxv, img.dtype)
else:
return (img * (1 + self.factor)).astype(img.dtype)
def __call__(self, img):
return rescale_array(img, self.minv, self.maxv, self.dtype)