"""Module for visualization functions.
Examples
--------
.. doctest-skip::
>>> import numpy as np
>>> from viqa.utils.visualization import visualize_2d, visualize_3d
>>> img = np.random.rand(100, 100)
>>> visualize_2d(img)
>>> img = np.random.rand(100, 100, 100)
>>> visualize_3d(img, (50, 50, 50))
"""
# Authors
# -------
# Author: Lukas Behammer
# Research Center Wels
# University of Applied Sciences Upper Austria, 2023
# CT Research Group
#
# Modifications
# -------------
# Original code, 2024, Lukas Behammer
#
# License
# -------
# BSD-3-Clause License
import matplotlib.patches as patches
import matplotlib.pyplot as plt
import numpy as np
from viqa.utils._module import try_import
widgets, has_ipywidgets = try_import("ipywidgets")
FIGSIZE_CNR_2D = (10, 5.5)
FIGSIZE_CNR_3D = (10, 8)
FIGSIZE_SNR_2D = (7, 7)
FIGSIZE_SNR_3D = (10, 4)
def _visualize_cnr_2d(
img,
signal_center,
background_center,
radius,
region_type,
export_path=None,
show=True,
**kwargs,
):
figsize = kwargs.pop("figsize", FIGSIZE_CNR_2D)
dpi = kwargs.pop("dpi", 300)
fig, axs = plt.subplots(1, 2, figsize=figsize, dpi=dpi)
fig.suptitle("Regions for CNR Calculation", y=0.92)
axs[0].imshow(img, cmap="gray")
axs[0].set_title("Background")
axs[0].set_xlabel("x")
axs[0].set_ylabel("y")
axs[0].invert_yaxis()
if region_type in ["cubic", "cube", "square"]:
patch_1 = patches.Rectangle(
(
background_center[0] - radius,
background_center[1] - radius,
),
radius * 2,
radius * 2,
linewidth=1,
edgecolor="#ca0020",
facecolor="none",
)
elif region_type in ["spherical", "sphere", "circle"]:
patch_1 = patches.Circle(
(background_center[0], background_center[1]),
radius,
linewidth=1,
edgecolor="#ca0020",
facecolor="none",
)
if patch_1:
axs[0].add_patch(patch_1)
axs[1].imshow(img[..., ::-1], cmap="gray")
axs[1].set_title("Signal")
axs[1].set_xlabel("x")
axs[1].set_ylabel("y")
axs[1].invert_yaxis()
if region_type in ["cubic", "cube", "square"]:
patch_2 = patches.Rectangle(
(
signal_center[0] - radius,
signal_center[1] - radius,
),
radius * 2,
radius * 2,
linewidth=1,
edgecolor="#0571b0",
facecolor="none",
)
elif region_type in ["spherical", "sphere", "circle"]:
patch_2 = patches.Circle(
(signal_center[0], signal_center[1]),
radius,
linewidth=1,
edgecolor="#0571b0",
facecolor="none",
)
if patch_2:
axs[1].add_patch(patch_2)
if show:
plt.show()
if export_path:
plt.savefig(export_path, bbox_inches="tight", pad_inches=0.5)
def _visualize_cnr_3d(
img,
signal_center,
background_center,
radius,
region_type,
export_path=None,
show=True,
**kwargs,
):
figsize = kwargs.pop("figsize", FIGSIZE_CNR_3D)
dpi = kwargs.pop("dpi", 300)
fig, axs = plt.subplots(2, 3, figsize=figsize, dpi=dpi, **kwargs)
fig.suptitle(
"Background (Upper) and Signal Region (Lower) for CNR Calculation", y=0.92
)
# Background Region
axs[0][0].imshow(np.rot90(img[background_center[0], :, ::-1]), cmap="gray")
axs[0][0].set_title(f"x-axis, slice: {background_center[0]}", c="#d7191c")
axs[0][0].set_xlabel("y")
axs[0][0].set_ylabel("z")
axs[0][0].invert_yaxis()
axs[0][0].axvline(x=background_center[1], color="#fdae61", linestyle="--")
axs[0][0].axhline(y=background_center[2], color="#2c7bb6", linestyle="--")
if region_type in ["cubic", "cube", "square"]:
patch_1 = patches.Rectangle(
(
background_center[1] - radius,
background_center[2] - radius,
),
radius * 2,
radius * 2,
linewidth=1,
edgecolor="#ffffbf",
facecolor="none",
)
elif region_type in ["spherical", "sphere", "circle"]:
patch_1 = patches.Circle(
(background_center[1], background_center[2]),
radius,
linewidth=1,
edgecolor="#ffffbf",
facecolor="none",
)
if patch_1:
axs[0][0].add_patch(patch_1)
axs[0][1].imshow(np.rot90(img[:, background_center[1], ::-1]), cmap="gray")
axs[0][1].set_title(f"y-axis, slice: {background_center[1]}", c="#fdae61")
axs[0][1].set_xlabel("x")
axs[0][1].set_ylabel("z")
axs[0][1].invert_yaxis()
axs[0][1].axvline(x=background_center[0], color="#d7191c", linestyle="--")
axs[0][1].axhline(y=background_center[2], color="#2c7bb6", linestyle="--")
if region_type in ["cubic", "cube", "square"]:
patch_2 = patches.Rectangle(
(
background_center[0] - radius,
background_center[2] - radius,
),
radius * 2,
radius * 2,
linewidth=1,
edgecolor="#ffffbf",
facecolor="none",
)
elif region_type in ["spherical", "sphere", "circle"]:
patch_2 = patches.Circle(
(background_center[0], background_center[2]),
radius,
linewidth=1,
edgecolor="#ffffbf",
facecolor="none",
)
if patch_2:
axs[0][1].add_patch(patch_2)
axs[0][2].imshow(np.rot90(img[::-1, :, background_center[2]], -1), cmap="gray")
axs[0][2].set_title(f"z-axis, slice: {background_center[2]}", c="#2c7bb6")
axs[0][2].set_xlabel("x")
axs[0][2].set_ylabel("y")
axs[0][2].invert_yaxis()
axs[0][2].axvline(x=background_center[0], color="#d7191c", linestyle="--")
axs[0][2].axhline(y=background_center[1], color="#fdae61", linestyle="--")
if region_type in ["cubic", "cube", "square"]:
patch_3 = patches.Rectangle(
(
background_center[0] - radius,
background_center[1] - radius,
),
radius * 2,
radius * 2,
linewidth=1,
edgecolor="#ffffbf",
facecolor="none",
)
elif region_type in ["spherical", "sphere", "circle"]:
patch_3 = patches.Circle(
(background_center[0], background_center[1]),
radius,
linewidth=1,
edgecolor="#ffffbf",
facecolor="none",
)
if patch_3:
axs[0][2].add_patch(patch_3)
# Signal Region
axs[1][0].imshow(np.rot90(img[signal_center[0], :, ::-1]), cmap="gray")
axs[1][0].set_title(f"x-axis, slice: {signal_center[0]}", c="#d7191c")
axs[1][0].set_xlabel("y")
axs[1][0].set_ylabel("z")
axs[1][0].invert_yaxis()
axs[1][0].axvline(x=signal_center[1], color="#fdae61", linestyle="--")
axs[1][0].axhline(y=signal_center[2], color="#2c7bb6", linestyle="--")
if region_type in ["cubic", "cube", "square"]:
patch_4 = patches.Rectangle(
(
signal_center[1] - radius,
signal_center[2] - radius,
),
radius * 2,
radius * 2,
linewidth=1,
edgecolor="#abd9e9",
facecolor="none",
)
elif region_type in ["spherical", "sphere", "circle"]:
patch_4 = patches.Circle(
(signal_center[1], signal_center[2]),
radius,
linewidth=1,
edgecolor="#abd9e9",
facecolor="none",
)
if patch_4:
axs[1][0].add_patch(patch_4)
axs[1][1].imshow(np.rot90(img[:, signal_center[1], ::-1]), cmap="gray")
axs[1][1].set_title(f"y-axis, slice: {signal_center[1]}", c="#fdae61")
axs[1][1].set_xlabel("x")
axs[1][1].set_ylabel("z")
axs[1][1].invert_yaxis()
axs[1][1].axvline(x=signal_center[0], color="#d7191c", linestyle="--")
axs[1][1].axhline(y=signal_center[2], color="#2c7bb6", linestyle="--")
if region_type in ["cubic", "cube", "square"]:
patch_5 = patches.Rectangle(
(
signal_center[0] - radius,
signal_center[2] - radius,
),
radius * 2,
radius * 2,
linewidth=1,
edgecolor="#abd9e9",
facecolor="none",
)
elif region_type in ["spherical", "sphere", "circle"]:
patch_5 = patches.Circle(
(signal_center[0], signal_center[2]),
radius,
linewidth=1,
edgecolor="#abd9e9",
facecolor="none",
)
if patch_5:
axs[1][1].add_patch(patch_5)
axs[1][2].imshow(np.rot90(img[::-1, :, signal_center[2]], -1), cmap="gray")
axs[1][2].set_title(f"z-axis, slice: {signal_center[2]}", c="#2c7bb6")
axs[1][2].set_xlabel("x")
axs[1][2].set_ylabel("y")
axs[1][2].invert_yaxis()
axs[1][2].axvline(x=signal_center[0], color="#d7191c", linestyle="--")
axs[1][2].axhline(y=signal_center[1], color="#fdae61", linestyle="--")
if region_type in ["cubic", "cube", "square"]:
patch_6 = patches.Rectangle(
(
signal_center[0] - radius,
signal_center[1] - radius,
),
radius * 2,
radius * 2,
linewidth=1,
edgecolor="#abd9e9",
facecolor="none",
)
elif region_type in ["spherical", "sphere", "circle"]:
patch_6 = patches.Circle(
(signal_center[0], signal_center[1]),
radius,
linewidth=1,
edgecolor="#abd9e9",
facecolor="none",
)
if patch_6:
axs[1][2].add_patch(patch_6)
if show:
plt.show()
if export_path:
plt.savefig(export_path, bbox_inches="tight", pad_inches=0.5)
def _visualize_snr_2d(
img,
signal_center,
radius,
region_type,
signal=None,
export_path=None,
show=True,
**kwargs,
):
if region_type not in [
"cubic",
"cube",
"square",
"spherical",
"sphere",
"circle",
"full",
"original",
]:
raise ValueError("Invalid region type.")
elif region_type == "full":
if signal is None:
region_type = "original"
elif signal.shape != img.shape:
raise ValueError("The signal must have the same shape as the image.")
figsize = kwargs.pop("figsize", FIGSIZE_SNR_2D)
dpi = kwargs.pop("dpi", 300)
fig, ax = plt.subplots(1, 1, figsize=figsize, dpi=dpi)
fig.suptitle("Signal Region for SNR Calculation", y=0.92)
ax.imshow(img[..., ::-1], cmap="gray")
if region_type == "full":
ax.imshow(signal, cmap="viridis", alpha=0.5)
ax.set_xlabel("x")
ax.set_ylabel("y")
ax.invert_yaxis()
if region_type in ["cubic", "cube", "square"]:
patch = patches.Rectangle(
(
signal_center[0] - radius,
signal_center[1] - radius,
),
radius * 2,
radius * 2,
linewidth=1,
edgecolor="#0571b0",
facecolor="none",
)
elif region_type in ["spherical", "sphere", "circle"]:
patch = patches.Circle(
(signal_center[0], signal_center[1]),
radius,
linewidth=1,
edgecolor="#0571b0",
facecolor="none",
)
else:
patch = None
if patch:
ax.add_patch(patch)
if show:
plt.show()
if export_path:
plt.savefig(export_path, bbox_inches="tight", pad_inches=0.5)
def _visualize_snr_3d(
img,
signal_center,
radius,
region_type,
signal=None,
export_path=None,
show=True,
**kwargs,
):
if region_type not in [
"cubic",
"cube",
"square",
"spherical",
"sphere",
"circle",
"full",
"original",
]:
raise ValueError("Invalid region type.")
elif region_type == "full":
if signal is None:
region_type = "original"
elif signal.shape != img.shape:
raise ValueError("The signal must have the same shape as the image.")
figsize = kwargs.pop("figsize", FIGSIZE_SNR_3D)
dpi = kwargs.pop("dpi", 300)
fig, axs = plt.subplots(1, 3, figsize=figsize, dpi=dpi)
fig.suptitle("Signal Region for SNR Calculation", y=0.92)
axs[0].imshow(np.rot90(img[signal_center[0], :, ::-1]), cmap="gray")
if region_type == "full":
axs[0].imshow(
np.rot90(signal[signal_center[0], :, ::-1]), cmap="viridis", alpha=0.5
)
axs[0].set_title(f"x-axis, slice: {signal_center[0]}", c="#d7191c")
axs[0].set_xlabel("y")
axs[0].set_ylabel("z")
axs[0].invert_yaxis()
axs[0].axvline(x=signal_center[1], color="#fdae61", linestyle="--")
axs[0].axhline(y=signal_center[2], color="#2c7bb6", linestyle="--")
if region_type in ["cubic", "cube", "square"]:
patch_1 = patches.Rectangle(
(
signal_center[1] - radius,
signal_center[2] - radius,
),
radius * 2,
radius * 2,
linewidth=1,
edgecolor="#ffffbf",
facecolor="none",
)
elif region_type in ["spherical", "sphere", "circle"]:
patch_1 = patches.Circle(
(signal_center[1], signal_center[2]),
radius,
linewidth=1,
edgecolor="#ffffbf",
facecolor="none",
)
else:
patch_1 = None
if patch_1:
axs[0].add_patch(patch_1)
axs[1].imshow(np.rot90(img[:, signal_center[1], ::-1]), cmap="gray")
if region_type == "full":
axs[1].imshow(
np.rot90(signal[:, signal_center[1], ::-1]), cmap="viridis", alpha=0.5
)
axs[1].set_title(f"y-axis, slice: {signal_center[1]}", c="#fdae61")
axs[1].set_xlabel("x")
axs[1].set_ylabel("z")
axs[1].invert_yaxis()
axs[1].axvline(x=signal_center[0], color="#d7191c", linestyle="--")
axs[1].axhline(y=signal_center[2], color="#2c7bb6", linestyle="--")
if region_type in ["cubic", "cube", "square"]:
patch_2 = patches.Rectangle(
(
signal_center[0] - radius,
signal_center[2] - radius,
),
radius * 2,
radius * 2,
linewidth=1,
edgecolor="#ffffbf",
facecolor="none",
)
elif region_type in ["spherical", "sphere", "circle"]:
patch_2 = patches.Circle(
(signal_center[0], signal_center[2]),
radius,
linewidth=1,
edgecolor="#ffffbf",
facecolor="none",
)
else:
patch_2 = None
if patch_2:
axs[1].add_patch(patch_2)
axs[2].imshow(np.rot90(img[::-1, :, signal_center[2]], -1), cmap="gray")
if region_type == "full":
axs[2].imshow(
np.rot90(signal[::-1, :, signal_center[2]], -1), cmap="viridis", alpha=0.5
)
axs[2].set_title(f"z-axis, slice: {signal_center[2]}", c="#2c7bb6")
axs[2].set_xlabel("x")
axs[2].set_ylabel("y")
axs[2].invert_yaxis()
axs[2].axvline(x=signal_center[0], color="#d7191c", linestyle="--")
axs[2].axhline(y=signal_center[1], color="#fdae61", linestyle="--")
if region_type in ["cubic", "cube", "square"]:
patch_3 = patches.Rectangle(
(
signal_center[0] - radius,
signal_center[1] - radius,
),
radius * 2,
radius * 2,
linewidth=1,
edgecolor="#ffffbf",
facecolor="none",
)
elif region_type in ["spherical", "sphere", "circle"]:
patch_3 = patches.Circle(
(signal_center[0], signal_center[1]),
radius,
linewidth=1,
edgecolor="#ffffbf",
facecolor="none",
)
else:
patch_3 = None
if patch_3:
axs[2].add_patch(patch_3)
if show:
plt.show()
if export_path:
plt.savefig(export_path, bbox_inches="tight", pad_inches=0.5)
def _create_slider_widget(**kwargs):
if not has_ipywidgets:
raise ImportError(
"ipywidgets is not installed. Please install it to use this function."
)
min_val = kwargs.pop("min", 0)
step = kwargs.pop("step", 1)
continuous_update = kwargs.pop("continuous_update", False)
slider = widgets.IntSlider(
min=min_val,
step=step,
continuous_update=continuous_update,
**kwargs,
)
return slider
[docs]
def visualize_2d(img, export_path=None, **kwargs):
"""
Visualize a 2D image.
The function visualizes a 2D image. If `export_path` is provided, the
visualization is saved to the specified path.
Parameters
----------
img : np.ndarray
The 2D image to visualize.
export_path : str or Path, optional
The path to save the visualization.
kwargs :
Additional keyword arguments for the plot. Passed to
``matplotlib.pyplot.imshow``.
Raises
------
ValueError
If the image is not 2D.
Returns
-------
None
"""
if img.ndim != 2:
raise ValueError("The image must be 2D.")
figsize = kwargs.pop("figsize", (6, 6))
dpi = kwargs.pop("dpi", 300)
plt.figure(figsize=figsize, dpi=dpi)
if "cmap" not in kwargs:
plt.imshow(img, cmap="gray", **kwargs)
else:
plt.imshow(img, **kwargs)
plt.xlabel("x")
plt.ylabel("y")
plt.gca().invert_yaxis()
plt.show()
if export_path:
plt.savefig(export_path, bbox_inches="tight", pad_inches=0.5)
[docs]
def visualize_3d(img, slices, export_path=None, **kwargs):
"""
Visualize 3D image slices in 3 different planes.
The function visualizes the 3D image slices in the ``x``, ``y`` and ``z`` direction.
If ``export_path`` is provided, the visualization is saved to the specified path.
Parameters
----------
img : np.ndarray
The 3D image to visualize.
slices : tuple
The slices to visualize in the ``x``, ``y`` and ``z`` direction. The slices must
be positive or negative integers.
export_path : str or Path, optional
The path to save the visualization.
kwargs :
Additional keyword arguments for the plot. Passed to
:py:func:`matplotlib.pyplot.subplots`.
Returns
-------
None
Raises
------
ValueError
If the number of slices is not 3 or if the slices are not integers.
If the image is not 3D.
If the slices are out of bounds.
"""
if len(slices) != 3:
raise ValueError("The number of slices must be 3.")
if not all(isinstance(slice_, int) for slice_ in slices):
raise ValueError("All slices must be integers.")
if img.ndim != 3:
raise ValueError("The image must be 3D.")
if not all(
-img.shape[i] <= slice_ <= img.shape[i] for i, slice_ in enumerate(slices)
):
raise ValueError("The slices are out of bounds.")
x = slices[0]
y = slices[1]
z = slices[2]
figsize = kwargs.pop("figsize", (14, 6))
dpi = kwargs.pop("dpi", 300)
_, axs = plt.subplots(1, 3, figsize=figsize, dpi=dpi, **kwargs)
axs[0].imshow(np.rot90(img[x, :, ::-1]), cmap="gray")
axs[0].set_xlabel("y")
axs[0].set_ylabel("z")
axs[0].invert_yaxis()
axs[0].axhline(y=z, color="#7570b3", linestyle="--")
axs[0].axvline(x=y, color="#d95f02", linestyle="--")
axs[0].set_title(f"x-axis, slice: {x}", c="#1b9e77")
axs[1].imshow(np.rot90(img[:, y, ::-1]), cmap="gray")
axs[1].set_xlabel("x")
axs[1].set_ylabel("z")
axs[1].invert_yaxis()
axs[1].axhline(y=z, color="#7570b3", linestyle="--")
axs[1].axvline(x=x, color="#1b9e77", linestyle="--")
axs[1].set_title(f"y-axis, slice: {y}", c="#d95f02")
axs[2].imshow(np.rot90(img[::-1, :, z], -1), cmap="gray")
axs[2].set_xlabel("x")
axs[2].set_ylabel("y")
axs[2].invert_yaxis()
axs[2].axhline(y=y, color="#d95f02", linestyle="--")
axs[2].axvline(x=x, color="#1b9e77", linestyle="--")
axs[2].set_title(f"z-axis, slice: {z}", c="#7570b3")
plt.show()
if export_path:
plt.savefig(export_path, bbox_inches="tight", pad_inches=0.5)