def mesh_to_mask(mesh: trimesh.Trimesh, R, grid_size):
mesh.vertices = mesh.vertices @ R.T
bottom_left = np.min(mesh.vertices[:,:2], axis = 0)
top_right = np.max(mesh.vertices[:,:2], axis = 0)
x = np.arange(bottom_left[0], top_right[0], grid_size)
y = np.arange(bottom_left[1], top_right[1], grid_size)
X, Y = np.meshgrid(x, y)
z = np.full_like(X, -5.0)
xyz = np.stack((X, Y, z), axis = 2).reshape((-1, 3))
d = np.zeros_like(xyz)
d[:,2] = 1
mask = mesh.ray.intersects_any(xyz, d)
mesh.vertices = mesh.vertices @ R
intersection_points, *_ = mesh.ray.intersects_location(xyz, d)
offset = np.mean(intersection_points, axis = 0)
u, s, vt = np.linalg.svd(xyz[mask,:2] - np.mean(xyz[mask,:2], axis = 0))
if vt[0,0] * vt[1,1] - vt[0,1] * vt[1,0] < 0:
vt[1,:] *= -1
if np.sum((xyz[mask,:2] - np.mean(xyz[mask,:2])) @ vt[0,:] < 0) > np.sum(mask) // 2:
vt = -vt
return mask.reshape(X.shape).T, offset, vt
def mesh_and_extract_largest_connected_surface(volume, level_set):
vertices, faces = marching_cubes(volume, level_set)
mesh = Trimesh()
mesh.vertices = vertices
mesh.faces = faces
meshes = mesh.split(only_watertight=False)
sorted_meshes = sorted(meshes, key=lambda x: len(x.vertices))
return sorted_meshes[-1]
def plot_hull_section_colours(
hull: trimesh.Trimesh, # type: ignore[name-defined] # noqa
model: Union[Literal["CAM02LCD", "CAM02SCD", "CAM02UCS", "CAM16LCD",
"CAM16SCD", "CAM16UCS", "CIE XYZ", "CIE xyY",
"CIE Lab", "CIE Luv", "CIE UCS", "CIE UVW", "DIN99",
"Hunter Lab", "Hunter Rdab", "ICaCb", "ICtCp", "IPT",
"IgPgTg", "Jzazbz", "OSA UCS", "Oklab", "hdr-CIELAB",
"hdr-IPT", ], str, ] = "CIE xyY",
axis: Union[Literal["+z", "+x", "+y"], str] = "+z",
origin: Floating = 0.5,
normalise: Boolean = True,
section_colours: Optional[Union[ArrayLike, str]] = None,
section_opacity: Floating = 1,
convert_kwargs: Optional[Dict] = None,
samples: Integer = 256,
**kwargs: Any,
) -> Tuple[plt.Figure, plt.Axes]:
"""
Plot the section colours of given *trimesh* hull along given axis and
origin.
Parameters
----------
hull
*Trimesh* hull.
model
Colourspace model, see :attr:`colour.COLOURSPACE_MODELS` attribute for
the list of supported colourspace models.
axis
Axis the hull section will be normal to.
origin
Coordinate along ``axis`` at which to plot the hull section.
normalise
Whether to normalise ``axis`` to the extent of the hull along it.
section_colours
Colours of the hull section, if ``section_colours`` is set to *RGB*,
the colours will be computed according to the corresponding
coordinates.
section_opacity
Opacity of the hull section colours.
convert_kwargs
Keyword arguments for the :func:`colour.convert` definition.
samples
Samples count on one axis when computing the hull section colours.
Other Parameters
----------------
kwargs
{:func:`colour.plotting.artist`,
:func:`colour.plotting.render`},
See the documentation of the previously listed definitions.
Returns
-------
:class:`tuple`
Current figure and axes.
Examples
--------
>>> from colour.models import RGB_COLOURSPACE_sRGB
>>> from colour.utilities import is_trimesh_installed
>>> vertices, faces, _outline = primitive_cube(1, 1, 1, 64, 64, 64)
>>> XYZ_vertices = RGB_to_XYZ(
... vertices['position'] + 0.5,
... RGB_COLOURSPACE_sRGB.whitepoint,
... RGB_COLOURSPACE_sRGB.whitepoint,
... RGB_COLOURSPACE_sRGB.matrix_RGB_to_XYZ,
... )
>>> if is_trimesh_installed:
... import trimesh
... hull = trimesh.Trimesh(XYZ_vertices, faces, process=False)
... plot_hull_section_colours(hull, section_colours='RGB')
... # doctest: +ELLIPSIS
(<Figure size ... with 1 Axes>, <...AxesSubplot...>)
.. image:: ../_static/Plotting_Plot_Hull_Section_Colours.png
:align: center
:alt: plot_hull_section_colours
"""
axis = validate_method(
axis,
["+z", "+x", "+y"],
'"{0}" axis is invalid, it must be one of {1}!',
)
hull = hull.copy()
settings: Dict[str, Any] = {"uniform": True}
settings.update(kwargs)
_figure, axes = artist(**settings)
section_colours = cast(
ArrayLike,
optional(section_colours,
HEX_to_RGB(CONSTANTS_COLOUR_STYLE.colour.average)),
)
convert_kwargs = optional(convert_kwargs, {})
# Luminance / Lightness reordered along "z" axis.
with suppress_warnings(python_warnings=True):
ijk_vertices = colourspace_model_axis_reorder(
convert(hull.vertices, "CIE XYZ", model, **convert_kwargs), model)
ijk_vertices = np.nan_to_num(ijk_vertices)
ijk_vertices *= COLOURSPACE_MODELS_DOMAIN_RANGE_SCALE_1_TO_REFERENCE[
model]
hull.vertices = ijk_vertices
if axis == "+x":
index_origin = 0
elif axis == "+y":
index_origin = 1
elif axis == "+z":
index_origin = 2
plane = MAPPING_AXIS_TO_PLANE[axis]
section = hull_section(hull, axis, origin, normalise)
padding = 0.1 * np.mean(
COLOURSPACE_MODELS_DOMAIN_RANGE_SCALE_1_TO_REFERENCE[model])
min_x = np.min(ijk_vertices[..., plane[0]]) - padding
max_x = np.max(ijk_vertices[..., plane[0]]) + padding
min_y = np.min(ijk_vertices[..., plane[1]]) - padding
max_y = np.max(ijk_vertices[..., plane[1]]) + padding
extent = (min_x, max_x, min_y, max_y)
use_RGB_section_colours = str(section_colours).upper() == "RGB"
if use_RGB_section_colours:
ii, jj = np.meshgrid(
np.linspace(min_x, max_x, samples),
np.linspace(max_y, min_y, samples),
)
ij = tstack([ii, jj])
ijk_section = full((samples, samples, 3),
np.median(section[..., index_origin]))
ijk_section[..., plane] = ij
ijk_section /= COLOURSPACE_MODELS_DOMAIN_RANGE_SCALE_1_TO_REFERENCE[
model]
XYZ_section = convert(
colourspace_model_axis_reorder(ijk_section, model, "Inverse"),
model,
"CIE XYZ",
**convert_kwargs,
)
RGB_section = XYZ_to_plotting_colourspace(XYZ_section)
else:
section_colours = np.hstack([section_colours, section_opacity])
facecolor = "none" if use_RGB_section_colours else section_colours
polygon = Polygon(
section[..., plane],
facecolor=facecolor,
edgecolor="none",
zorder=CONSTANTS_COLOUR_STYLE.zorder.background_polygon,
)
axes.add_patch(polygon)
if use_RGB_section_colours:
image = axes.imshow(
np.clip(RGB_section, 0, 1),
interpolation="bilinear",
extent=extent,
clip_path=None,
alpha=section_opacity,
zorder=CONSTANTS_COLOUR_STYLE.zorder.background_polygon,
)
image.set_clip_path(polygon)
settings = {
"axes": axes,
"bounding_box": extent,
}
settings.update(kwargs)
return render(**settings)
def plot_hull_section_contour(
hull: trimesh.Trimesh, # type: ignore[name-defined] # noqa
model: Union[Literal["CAM02LCD", "CAM02SCD", "CAM02UCS", "CAM16LCD",
"CAM16SCD", "CAM16UCS", "CIE XYZ", "CIE xyY",
"CIE Lab", "CIE Luv", "CIE UCS", "CIE UVW", "DIN99",
"Hunter Lab", "Hunter Rdab", "ICaCb", "ICtCp", "IPT",
"IgPgTg", "Jzazbz", "OSA UCS", "Oklab", "hdr-CIELAB",
"hdr-IPT", ], str, ] = "CIE xyY",
axis: Union[Literal["+z", "+x", "+y"], str] = "+z",
origin: Floating = 0.5,
normalise: Boolean = True,
contour_colours: Optional[Union[ArrayLike, str]] = None,
contour_opacity: Floating = 1,
convert_kwargs: Optional[Dict] = None,
**kwargs: Any,
) -> Tuple[plt.Figure, plt.Axes]:
"""
Plot the section contour of given *trimesh* hull along given axis and
origin.
Parameters
----------
hull
*Trimesh* hull.
model
Colourspace model, see :attr:`colour.COLOURSPACE_MODELS` attribute for
the list of supported colourspace models.
axis
Axis the hull section will be normal to.
origin
Coordinate along ``axis`` at which to plot the hull section.
normalise
Whether to normalise ``axis`` to the extent of the hull along it.
contour_colours
Colours of the hull section contour, if ``contour_colours`` is set to
*RGB*, the colours will be computed according to the corresponding
coordinates.
contour_opacity
Opacity of the hull section contour.
convert_kwargs
Keyword arguments for the :func:`colour.convert` definition.
Other Parameters
----------------
kwargs
{:func:`colour.plotting.artist`,
:func:`colour.plotting.render`},
See the documentation of the previously listed definitions.
Returns
-------
:class:`tuple`
Current figure and axes.
Examples
--------
>>> from colour.models import RGB_COLOURSPACE_sRGB
>>> from colour.utilities import is_trimesh_installed
>>> vertices, faces, _outline = primitive_cube(1, 1, 1, 64, 64, 64)
>>> XYZ_vertices = RGB_to_XYZ(
... vertices['position'] + 0.5,
... RGB_COLOURSPACE_sRGB.whitepoint,
... RGB_COLOURSPACE_sRGB.whitepoint,
... RGB_COLOURSPACE_sRGB.matrix_RGB_to_XYZ,
... )
>>> if is_trimesh_installed:
... import trimesh
... hull = trimesh.Trimesh(XYZ_vertices, faces, process=False)
... plot_hull_section_contour(hull, contour_colours='RGB')
... # doctest: +ELLIPSIS
(<Figure size ... with 1 Axes>, <...AxesSubplot...>)
.. image:: ../_static/Plotting_Plot_Hull_Section_Contour.png
:align: center
:alt: plot_hull_section_contour
"""
hull = hull.copy()
contour_colours = cast(
Union[ArrayLike, str],
optional(contour_colours, CONSTANTS_COLOUR_STYLE.colour.dark),
)
settings: Dict[str, Any] = {"uniform": True}
settings.update(kwargs)
_figure, axes = artist(**settings)
convert_kwargs = optional(convert_kwargs, {})
# Luminance / Lightness is re-ordered along "z-up" axis.
with suppress_warnings(python_warnings=True):
ijk_vertices = colourspace_model_axis_reorder(
convert(hull.vertices, "CIE XYZ", model, **convert_kwargs), model)
ijk_vertices = np.nan_to_num(ijk_vertices)
ijk_vertices *= COLOURSPACE_MODELS_DOMAIN_RANGE_SCALE_1_TO_REFERENCE[
model]
hull.vertices = ijk_vertices
plane = MAPPING_AXIS_TO_PLANE[axis]
padding = 0.1 * np.mean(
COLOURSPACE_MODELS_DOMAIN_RANGE_SCALE_1_TO_REFERENCE[model])
min_x = np.min(ijk_vertices[..., plane[0]]) - padding
max_x = np.max(ijk_vertices[..., plane[0]]) + padding
min_y = np.min(ijk_vertices[..., plane[1]]) - padding
max_y = np.max(ijk_vertices[..., plane[1]]) + padding
extent = (min_x, max_x, min_y, max_y)
use_RGB_contour_colours = str(contour_colours).upper() == "RGB"
section = hull_section(hull, axis, origin, normalise)
if use_RGB_contour_colours:
ijk_section = section / (
COLOURSPACE_MODELS_DOMAIN_RANGE_SCALE_1_TO_REFERENCE[model])
XYZ_section = convert(
colourspace_model_axis_reorder(ijk_section, model, "Inverse"),
model,
"CIE XYZ",
**convert_kwargs,
)
contour_colours = np.clip(XYZ_to_plotting_colourspace(XYZ_section), 0,
1)
section = np.reshape(section[..., plane], (-1, 1, 2))
line_collection = LineCollection(
np.concatenate([section[:-1], section[1:]], axis=1),
colors=contour_colours,
alpha=contour_opacity,
zorder=CONSTANTS_COLOUR_STYLE.zorder.background_line,
)
axes.add_collection(line_collection)
settings = {
"axes": axes,
"bounding_box": extent,
}
settings.update(kwargs)
return render(**settings)
angiogram_crop = np.zeros(angiogram.shape)
angiogram_crop[15:-60, :, 150:angiogram.shape[2] - 150] = angio_top
# angiogram_crop = angiogram_crop*angiogram_HU
# # TEST (Trimesh)
for im in angiogram_crop:
im[0, :] = 1
im[:, 0] = 1
v, f = make_mesh(angiogram_crop[2])
v, f = remesh.subdivide(v, f)
CTmesh = Trimesh()
CTmesh.vertices = v
CTmesh.faces = f
cta_mesh = smoothing.filter_humphrey(CTmesh)
cta_voxel = cta_mesh.voxelized(1)
cta_voxel = cta_voxel.fill()
cta_voxel = cta_voxel.revoxelized(
(angiogram_crop.shape[2], angiogram_crop.shape[1], 20 * 10))
cta_bone = cta_voxel.matrix
angiogram_test = np.zeros(
(cta_bone.shape[2], cta_bone.shape[1], cta_bone.shape[0]))
for i in range(cta_bone.shape[2]):
a = cta_bone[:, :, i]
