def draw_one(self, title, Lx, Ly, Lz, X, Y, Z, f, iso,
elev=None, azim=None):
""" Draw a single plot
title: title of the plot
X, Y, Z: 1D axes data
f: 3D data set (C style index?!)
"""
self.clf()
vert, face = measure.marching_cubes(f, iso)
self.rescale(vert, X, Y, Z, f.shape)
self.ax = self.add_subplot(111, projection='3d')
cmap, col = self.getcolor(vert, face)
surface = Poly3DCollection(vert[face])
surface.set_color(col)
surface.set_edgecolor('')
self.ax.add_collection3d(surface)
self.ax.set_xlabel(Lx, fontsize=14)
self.ax.set_ylabel(Ly, fontsize=14)
self.ax.set_zlabel(Lz, fontsize=14)
self.ax.set_xlim(X[0], X[-1])
self.ax.set_ylim(Y[0], Y[-1])
self.ax.set_zlim(Z[0], Z[-1])
self.ax.set_title(title)
self.ax.view_init(elev, azim)
self.colorbar(cmap, shrink=0.8, fraction=0.1, label=r'V $^2$')
self.tight_layout()
self.canvas.draw()
def plot_surface(voxels, voxel_size = 0.1):
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
# First grid the data
res = np.amax(voxels[1,:] - voxels[0,:])
ux = np.unique(voxels[:,0])
uy = np.unique(voxels[:,1])
uz = np.unique(voxels[:,2])
# Expand the model by one step in each direction
ux = np.hstack((ux[0] - res, ux, ux[-1] + res))
uy = np.hstack((uy[0] - res, uy, uy[-1] + res))
uz = np.hstack((uz[0] - res, uz, uz[-1] + res))
# Convert to a grid
X, Y, Z = np.meshgrid(ux, uy, uz)
# Create an empty voxel grid, then fill in the elements in voxels
V = np.zeros(X.shape)
N = voxels.shape[0]
for ii in xrange(N):
ix = ux == voxels[ii,0]
iy = uy == voxels[ii,1]
iz = uz == voxels[ii,2]
V[iy, ix, iz] = 1
marching_cubes = measure.marching_cubes(V, 0, spacing=(voxel_size, voxel_size, voxel_size))
verts = marching_cubes[0]
faces = marching_cubes[1]
ax.plot_trisurf(verts[:, 0], verts[:,1], faces, verts[:, 2], lw=0, color='red')
axis_equal(ax, verts[:, 0], verts[:,1], verts[:,2])
plt.show()
def tsdf2mesh(voxel_size, origin, tsdf_vol):
verts, faces, norms, vals = measure.marching_cubes(tsdf_vol, level=0)
verts = verts * voxel_size + origin # voxel grid coordinates to world coordinates
mesh = trimesh.Trimesh(vertices=verts,
faces=faces,
vertex_normals=norms)
return mesh
def load_nii_file(fname, threshold=0.5):
"""Uses the marching cube algorithm to turn a .nii binary mask into a surface weighted point cloud."""
mask = sitk.GetArrayFromImage(sitk.ReadImage(fname))
# mask = skimage.transform.downscale_local_mean(mask, (4,4,4))
verts, faces, normals, values = marching_cubes(mask, threshold)
return to_measure(verts, faces)
def plot_3d_image(ax, image, threshold=0.5, *args, **kwargs):
vertices, faces = measure.marching_cubes(image, level=threshold)[:2]
mesh = Poly3DCollection(vertices[faces], **kwargs)
ax.add_collection3d(mesh)
ax.set_xlabel("x")
ax.set_ylabel("y")
ax.set_zlabel("z")
set_equal_3d_axis(ax, vertices)
def test_marching_cubes_isotropic():
ellipsoid_isotropic = ellipsoid(6, 10, 16, levelset=True)
_, surf = ellipsoid_stats(6, 10, 16)
verts, faces = marching_cubes(ellipsoid_isotropic, 0.)
surf_calc = mesh_surface_area(verts, faces)
# Test within 1% tolerance for isotropic. Will always underestimate.
assert surf > surf_calc and surf_calc > surf * 0.99
def make_mesh(image, threshold=-300, step_size=1):
print "Transposing surface"
p = image.transpose(2,1,0)
print "Calculating surface"
verts, faces, norm, val = measure.marching_cubes(p, threshold, step_size=step_size, allow_degenerate=True)
return verts, faces
def march_the_cubes(data, aff):
from skimage.measure import marching_cubes
import numpy as np
from dipy.tracking.utils import move_streamlines
verts, faces = marching_cubes(data, level=0.5)
verts = np.asarray(list(move_streamlines(verts, aff)))
#TODO: apply affine here
return verts, faces
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 test_marching_cubes_isotropic():
ellipsoid_isotropic = ellipsoid(6, 10, 16, levelset=True)
_, surf = ellipsoid_stats(6, 10, 16)
verts, faces = marching_cubes(ellipsoid_isotropic, 0.)
surf_calc = mesh_surface_area(verts, faces)
# Test within 1% tolerance for isotropic. Will always underestimate.
assert surf > surf_calc and surf_calc > surf * 0.99
def march_cube(volume, level):
"""
help method for the march cube, using the skimage module
"""
verts, faces = measure.marching_cubes(volume,
level,
spacing=(1, 1, 1))
return verts, faces
def march_the_cubes(data, aff):
from skimage.measure import marching_cubes
import numpy as np
from dipy.tracking.utils import move_streamlines
verts, faces = marching_cubes(data, level=0.5)
verts = np.asarray(list(move_streamlines(verts, aff)))
#TODO: apply affine here
return verts, faces
def _extract_surface(pot_field, val, res, spacing):
from skimage import measure
vertices, simplices, normals, values = measure.marching_cubes(pot_field.reshape(res[0], res[1], res[2]),
val # , #0.2424792, # -0.559606
# spacing=spacing, # (10.0, 10.0, 10.0)
)
return vertices, simplices, normals, values
def test_both_algs_same_result_ellipse():
# Performing this test on data that does not have ambiguities
sphere_small = ellipsoid(1, 1, 1, levelset=True)
vertices1, faces1 = marching_cubes(sphere_small, 0, method='_lorensen')[:2]
vertices2, faces2 = marching_cubes(sphere_small, 0,
allow_degenerate=False)[:2]
vertices3, faces3 = marching_cubes(sphere_small,
0,
allow_degenerate=False,
method='lorensen')[:2]
# Order is different, best we can do is test equal shape and same
# vertices present
assert _same_mesh(vertices1, faces1, vertices2, faces2)
assert _same_mesh(vertices1, faces1, vertices3, faces3)
def plot_3D_image(3D_image,threshold=-300):
p = 3D_image.transpose(2,1,0)
verts, faces,normals, values = measure.marching_cubes(p, threshold, spacing=(0.1, 0.1, 0.1))
fig = plt.figure(figsize=(10, 10))
ax = fig.add_subplot(111, projection='3d')
ax.plot_trisurf(verts[:, 0], verts[:,1], faces, verts[:, 2],cmap='Spectral', lw=1)
plt.show()
def plot_3d_seg(image,name,threshold=1,save=False):
# Position the scan upright,
# so the head of the patient would be at the top facing the camera
check = np.max(np.unique(image))>1
verts, faces = measure.marching_cubes(image,threshold-1)
if check:
verts2, faces2 = measure.marching_cubes(image,threshold)
fig = plt.figure(figsize=(15, 15))
ax = fig.add_subplot(111, projection='3d')
# Fancy indexing: `verts[faces]` to generate a collection of triangles
mesh = Poly3DCollection(verts[faces], alpha=0.3)
if check:
mesh2 = Poly3DCollection(verts2[faces2], alpha=0.3)
face_color = [1, 0.2, 0.2]
if check:
face_color2 = [0.3, 0.3, 1]
mesh.set_facecolor(face_color)
if check:
mesh2.set_facecolor(face_color2)
ax.add_collection3d(mesh)
if check:
ax.add_collection3d(mesh2)
mesh_z = np.mean(image,axis=2)
#mesh_y = np.mean(image,axis=1)
#mesh_x = np.mean(image,axis=0)
X=np.linspace(0,image.shape[0]-1,image.shape[0])
Y=np.linspace(0,image.shape[1]-1,image.shape[1])
Z=np.linspace(0,image.shape[2]-1,image.shape[2])
#a,b=np.meshgrid(Y,Z)
c,d=np.meshgrid(X,Y)
#e,f=np.meshgrid(X,Z)
cest = ax.contourf(c,d, np.transpose(mesh_z), zdir='z', offset=0, cmap="Blues")
#cest = ax.contourf(np.transpose(mesh_x),b,a,zdir='x', offset=0, cmap="Greys")
#cest = ax.contourf(e,np.transpose(mesh_y),f,zdir="y", offset=image.shape[1], cmap="Greys")
ax.tick_params(axis='both', which='major', labelsize=18)
ax.set_ylim(0, image.shape[1])
ax.set_xlim(0, image.shape[0])
ax.set_zlim(0, image.shape[2])
ax.set_title(name+": 3D nodules and liver")
if save:
fig.savefig("/home/nnk/Bachelor/LiTS/Liver_segmentations/"+name+"_3D_nodules_and_liver.png", bbox_inches='tight')
plt.close(fig)
del mesh, verts, faces, face_color
if check:
del mesh2, verts2, faces2, face_color2
def test_marching_cubes_anisotropic():
spacing = (1.0, 10 / 6.0, 16 / 6.0)
ellipsoid_anisotropic = ellipsoid(6, 10, 16, spacing=spacing, levelset=True)
_, surf = ellipsoid_stats(6, 10, 16)
verts, faces = marching_cubes(ellipsoid_anisotropic, 0.0, spacing=spacing)
surf_calc = mesh_surface_area(verts, faces)
# Test within 1.5% tolerance for anisotropic. Will always underestimate.
assert surf > surf_calc and surf_calc > surf * 0.985
def update_segmentation_slices(selected, annotations):
ctx = dash.callback_context
# When shape annotations are changed, reset segmentation visualization
if (ctx.triggered[0]["prop_id"] == "annotations.data"
or annotations is None or annotations.get("x") is None
or annotations.get("z") is None):
mask = np.zeros_like(med_img)
overlay1 = slicer1.create_overlay_data(mask)
overlay2 = slicer2.create_overlay_data(mask)
return go.Mesh3d(), overlay1, overlay2
elif selected is not None and "range" in selected:
if len(selected["points"]) == 0:
return dash.no_update
v_min, v_max = selected["range"]["x"]
t_start = time()
# Horizontal mask
path = path_to_coords(annotations["z"]["path"])
rr, cc = draw.polygon(path[:, 1] / spacing[1], path[:, 0] / spacing[2])
mask = np.zeros(img.shape[1:])
mask[rr, cc] = 1
mask = ndimage.binary_fill_holes(mask)
# top and bottom, the top is a lower number than the bottom because y values
# increase moving down the figure
top, bottom = sorted(
[int(annotations["x"][c] / spacing[0]) for c in ["y0", "y1"]])
img_mask = np.logical_and(med_img > v_min, med_img <= v_max)
img_mask[:top] = False
img_mask[bottom:] = False
img_mask[top:bottom, np.logical_not(mask)] = False
img_mask = largest_connected_component(img_mask)
# img_mask_color = mask_to_color(img_mask)
t_end = time()
print("build the mask", t_end - t_start)
t_start = time()
# Update 3d viz
verts, faces, _, _ = measure.marching_cubes(filters.median(
img_mask, selem=np.ones((1, 7, 7))),
0.5,
step_size=3)
t_end = time()
print("marching cubes", t_end - t_start)
x, y, z = verts.T
i, j, k = faces.T
trace = go.Mesh3d(x=z,
y=y,
z=x,
color="red",
opacity=0.8,
i=k,
j=j,
k=i)
overlay1 = slicer1.create_overlay_data(img_mask)
overlay2 = slicer2.create_overlay_data(img_mask)
# todo: do we need an output to trigger an update?
return trace, overlay1, overlay2
else:
return (dash.no_update, ) * 3
def measure_surface_dist_real_size(struct1, struct2, pixdim):
"""
:param struct1: ndarray of 3D image 1 (the result of nib.get_data())
:param struct2: ndarray of 3D image 2 (the result of nib.get_data())
:param pixdim:
:return: Averaged Euclidan distance between the structures surface points (in mm)
"""
voxel_size = [pixdim[2], pixdim[1], pixdim[3]]
verts1, faces1, normals1, values1 = measure.marching_cubes(struct1, 0.5)
verts2, faces2, normals2, values2 = measure.marching_cubes(struct2, 0.5)
min_s_dist_array = np.zeros(verts1.shape[0])
for ind, surface_point in enumerate(verts1):
min_s_dist_array[ind] = min(
np.linalg.norm(((verts2 - surface_point) * voxel_size), axis=1))
mean_surface_dist = np.mean(min_s_dist_array)
return mean_surface_dist
def make_mesh(image, threshold=-500, step_size=1):
p = image.transpose(2, 1, 0)
verts, faces, norm, val = measure.marching_cubes(p,
threshold,
step_size=step_size,
allow_degenerate=True)
return verts, faces
def plot_3d(image_1, image_2, threshold=-300):
# Position the scan upright,
# so the head of the patient would be at the top facing the camera
try:
print('Plotting...')
global first_pass
first_pass = '******'
p_1 = image_1.transpose(2, 1, 0)
verts1, faces1 = measure.marching_cubes(p_1, threshold)
fig = plt.figure(figsize=(10, 10))
ax1 = fig.add_subplot(121, projection='3d')
# Fancy indexing: `verts[faces]` to generate a collection of triangles
mesh1 = Poly3DCollection(verts1[faces1], alpha=0.70)
face_color = [0.45, 0.45, 0.75]
mesh1.set_facecolor(face_color)
#return mesh
ax1.add_collection3d(mesh1)
ax1.set_xlim(0, p_1.shape[0])
ax1.set_ylim(0, p_1.shape[1])
ax1.set_zlim(0, p_1.shape[2])
p_2 = image_2.transpose(2, 1, 0)
verts2, faces2 = measure.marching_cubes(p_2, threshold)
ax2 = fig.add_subplot(122, projection='3d')
mesh2 = Poly3DCollection(verts2[faces2], alpha=0.70)
mesh2.set_facecolor(face_color)
ax2.add_collection3d(mesh2)
ax2.set_xlim(0, p_2.shape[0])
ax2.set_ylim(0, p_2.shape[1])
ax2.set_zlim(0, p_2.shape[2])
print('Done!')
first_pass = '******'
except:
print('Problem Plotting Graph...\n ABORT')
first_pass = '******'
return fig
def _compute_shape_size_features(self):
""" compute volume under a given mask"""
# mask volume
vox_size_SRC = 0.1 * np.array(self._IG.samplingSRC) # unit: cm
vox_vol = np.prod(vox_size_SRC) # unit: cm^
vol_cm3 = np.sum(self._maskImage_ndarray) * vox_vol # unit: ml or cm^3
self._df_feature_output['ShapeSize_vol_cm3'] = vol_cm3
# mask surface area
the_tumor_vol = np.zeros(self._inputImage_ndarray.shape)
the_tumor_vol[self._maskImage_ndarray] = self._inputImage_ndarray[
self._maskImage_ndarray]
verts, faces = skm.marching_cubes(the_tumor_vol, 0.0,
tuple(vox_size_SRC))
surf_area_cm2 = skm.mesh_surface_area(verts, faces) # unit: cm^2
self._df_feature_output['ShapeSize_surf_area_cm2'] = surf_area_cm2
self._df_feature_output['ShapeSize_compactness1'] = vol_cm3 / (
np.sqrt(np.pi) * surf_area_cm2**(2. / 3.))
self._df_feature_output['ShapeSize_compactness2'] = (
36. * np.pi * vol_cm3**2) / (surf_area_cm2**3)
self._df_feature_output['ShapeSize_sphericity'] = (np.pi**(
1. / 3.)) * (6 * vol_cm3)**(2. / 3.) / surf_area_cm2
self._df_feature_output[
'ShapeSize_surface2volratio'] = surf_area_cm2 / vol_cm3
# maximum 3D euclidean distance (or diameter?)
kk, ii, jj = np.where(self._maskImage_ndarray == True)
# skip computing max euclidean distance if the mask is too big such as including skin and etc.
if len(kk) > 300000 and vol_cm3 > 70.:
print '::ImageFeature:: compute_shape_size_feature, tumor mask is TOO big (vol: {} ml)! will not compute euc max distance :/'.format(
vol_cm3)
else:
print '::ImageFeature:: max euc distance # of voxels to go through: {}, vol = {} cm3'.format(
len(kk), vol_cm3)
eucdis_tmp = np.zeros((len(kk), 1))
for n in range(len(kk) - 1):
px1 = np.column_stack((kk[n + 1:], ii[n + 1:], jj[n + 1:]))
px2 = np.tile(np.array([kk[n], ii[n], jj[n]]),
(px1.shape[0], 1))
vox_size_tile = np.tile(vox_size_SRC, (px1.shape[0], 1))
eucdis = np.sqrt(
np.sum(((px1 - px2) * vox_size_tile)**2, axis=1))
eucdis_tmp[n] = np.amax(eucdis)
max_euc_dis = np.amax(eucdis_tmp)
self._df_feature_output['ShapeSize_max_euc_dis'] = max_euc_dis
# R is the radius of the sphere with the same volume as the tumor
tumor_sphere_R = (3 * vol_cm3 / (4 * np.pi))**(1. / 3)
self._df_feature_output[
'ShapeSize_spherical_disproportion'] = surf_area_cm2 / (
4 * np.pi * tumor_sphere_R**2)
print '::ImageFeature:: complete compute_shape_size_features!'
def mask2mesh(mask, mesh_processing=None, voxel_size=(1.0, 1.0, 1.0), level=0, step_size=2, preprocessing=None):
# apply volume preprocessing
mask = mask if preprocessing is None else preprocessing(mask)
# create mesh using marching cubes
vertx, faces, normals, _ = measure.marching_cubes(mask, level=level, spacing=voxel_size, step_size=step_size)
# if no mesh processing is defined returns tuple with marching cubes outputs
mesh = (vertx, faces, normals) if mesh_processing is None else mesh_processing(vertx, faces, normals)
return mesh
def extract_and_save_object(
image, output_file_name, voxel_size, threshold=0, step_size=1
):
verts, faces, normals, values = measure.marching_cubes(
image, threshold, step_size=step_size
)
verts, faces = convert_obj_to_br(verts, faces, voxel_size)
marching_cubes_to_obj(
(verts, faces, normals, values), str(output_file_name)
)
def make_mesh(self, threshold=400, step_size=1):
images = self.resample()
result = dict()
for key, image in images.items():
p = image.transpose(2, 1, 0)
verts, faces, norm, val = measure.marching_cubes(p, threshold, step_size=step_size, allow_degenerate=True)
result[key] = (verts, faces)
return result
def tsdf2mesh(tsdf_vol, mesh_path):
tsdf_vol = np.transpose(tsdf_vol, (1, 0, 2))
# Marching cubes
verts, faces, norms, vals = measure.marching_cubes(tsdf_vol, level=0.0)
# Get vertex colors
colors = np.array([(186 // 2, 176 // 2, 172 // 2)
for _ in range(verts.shape[0])],
dtype=np.uint8)
meshwrite(mesh_path, verts, faces, norms, colors)
def test_masked_marching_cubes():
ellipsoid_scalar = ellipsoid(6, 10, 16, levelset=True)
mask = np.ones_like(ellipsoid_scalar, dtype=bool)
mask[:10, :, :] = False
mask[:, :, 20:] = False
ver, faces, _, _ = marching_cubes(ellipsoid_scalar, 0, mask=mask)
area = mesh_surface_area(ver, faces)
assert_allclose(area, 299.56878662109375, rtol=.01)
def from_volume(self, voxel_grid, level=0):
'''
generates a mesh from a volume voxel_grid, using marching cubes
voxel_grid should be a voxel grid object.
This allows for the coordinates of the found mesh to be in world space.
'''
temp_verts, temp_faces = marching_cubes(voxel_grid.V, level)
self.vertices = voxel_grid.idx_to_world(temp_verts)
self.faces = temp_faces
def make_meshNew(image, threshold=-100, step_size=1):
# Generates a mesh from a stack of images (image variable)
print "Transposing surface"
# p = image.transpose(2,1,0)
p = image
print "Calculating surface"
try:
if (threshold == 0.0):
verts, faces = measure.marching_cubes(p)
else:
verts, faces = measure.marching_cubes(p, threshold)
except:
if (threshold == 0.0):
verts, faces = measure.marching_cubes_classic(p)
else:
verts, faces = measure.marching_cubes_classic(p, threshold)
return verts, faces
def make_outer_surface(filled_file, output_surface_file, se_diameter=15):
if os.path.isfile(output_surface_file):
log.info('Dural surface mesh %s already exists' %
os.path.basename(output_surface_file))
return
# read MRI
volume = nbfs.MGHImage.from_filename(filled_file)
volume = volume.get_data()
# change elements from {0,1} to {0,255}
volume *= 255
# Gaussian filter (sigma=1mm)
gaussian_volume = scimage.gaussian_filter(
volume, 1, mode='constant') # Is this correct?
# Binarize filtered image
avg = gaussian_volume.mean()
gaussian_volume[gaussian_volume > avg] = 255
gaussian_volume[gaussian_volume < avg] = 0
# Morphological closing:
# Construct structuring element
xx, yy = np.meshgrid(list(range(-1 * se_diameter + 1, se_diameter)),
list(range(-1 * se_diameter + 1, se_diameter)))
se = (xx**2 + yy**2) < se_diameter**2
# Take closing
closed_volume = np.stack([
scimage.grey_closing(
gaussian_volume[..., i], structure=se, mode='constant')
for i in range(gaussian_volume.shape[-1])
],
axis=-1)
# Binarize closed image
thresh = closed_volume.max() / 2
closed_volume[closed_volume <= thresh] = 0
closed_volume[closed_volume > thresh] = 255
# vertices,faces = isosurface(*,100)
vertices, faces, _, _ = measure.marching_cubes(closed_volume, 100)
# Reorient
v2 = np.zeros(vertices.shape)
v2[:, 0] = 129 - vertices[:, 0]
v2[:, 1] = vertices[:, 2] - 129
v2[:, 2] = 129 - vertices[:, 1]
vertices = v2
# Write geometry file
nbfs.write_geometry(output_surface_file, vertices, faces)
def __build_mesh(self, image, threshold=300, step_size=1):
'''
Helper method to build mesh for given 3D scan
'''
print("Transposing surface")
p = image.transpose(2, 1, 0)
print("Generating mesh")
verts, faces, _, _ = measure.marching_cubes(p, threshold,
step_size=step_size)#,
#allow_degenerate=True)
return verts, faces, p
def calculate_burning_area_3d(regression_map, regression_depth, mc_mask,
volume_ratio):
regression_depth = regression_depth / volume_ratio
verts, faces, norm, line = measure.marching_cubes(
regression_map,
level=regression_depth,
mask=mc_mask,
spacing=(volume_ratio, volume_ratio,
volume_ratio)) # (hide false values)
burning_area = measure.mesh_surface_area(verts, faces)
return burning_area
def reconstruction(structured_implicit,
resolution, b_min, b_max,
use_octree=False, num_samples=10000,
marching_cube=True):
'''
Reconstruct meshes from sdf predicted by the network.
:param structured_implicit: a StructuredImplicit object.
:param resolution: resolution of the grid cell
:param b_min: bounding box corner [x_min, y_min, z_min]
:param b_max: bounding box corner [x_max, y_max, z_max]
:param use_octree: whether to use octree acceleration
:param num_samples: how many points to query each gpu iteration
:return: marching cubes results.
'''
# First we create a grid by resolution
# and transforming matrix for grid coordinates to real world xyz
coords, mat = create_grid(resolution, resolution, resolution,
b_min, b_max)
# Then we define the lambda function for cell evaluation
def eval_func(points, structured_implicit):
points = np.expand_dims(points, axis=0)
samples = torch.from_numpy(points).to(device=structured_implicit.device).float()
samples = samples.transpose(-1, -2)
samples = samples.expand(structured_implicit.batch_size, -1, -1)
pred = structured_implicit.class_at_samples(samples, apply_class_transfer=False)[0][..., 0]
return pred.detach().cpu().numpy()
# Then we evaluate the grid
if use_octree:
sdf = []
for s in structured_implicit.unbind():
sdf.append(eval_grid_octree(coords, lambda p:eval_func(p, s), num_samples=num_samples).squeeze())
sdf = np.stack(sdf)
else:
sdf = eval_grid(coords, lambda p:eval_func(p, structured_implicit),
num_samples=num_samples, batch_size=structured_implicit.batch_size)
# Finally we do marching cubes
if marching_cube:
mesh = []
for s in sdf:
try:
verts, faces, _, _ = measure.marching_cubes(s, -0.07)
# transform verts into world coordinate system
verts = np.matmul(mat[:3, :3], verts.T) + mat[:3, 3:4]
verts = verts.T
mesh.append(trimesh.Trimesh(vertices=verts, faces=faces))
except (ValueError, RuntimeError) as e:
print('Failed to extract mesh with error %s. Setting to unit sphere.' % repr(e))
mesh.append(trimesh.primitives.Sphere(radius=0.5))
return mesh
else:
return sdf, mat
def getModel(self):
cloudField = self.cloudSet.getCloud()
verts, faces, normals, values = (np.array((), dtype=np.float32)
for i in range(4))
if np.any(cloudField > 0.1):
verts, faces, normals, values = measure.marching_cubes(
cloudField, 0.1)
# edges = self.cloudSet.getEdgeStrength(verts)
# verts, faces, normals, edges = self.decimate(verts, faces, normals, edges, 3)
return verts, faces, normals
def seg2mesh(idx, segmentation, step_size=1):
mask = segmentation == idx
_z, _x, _y = np.nonzero(mask)
# returns True only if mask is not flat in any dimension
if abs(_z.max() - _z.min()) > 1 and abs(_x.max() - _x.min()) > 1 and abs(
_y.max() - _y.min()) > 1:
coords, faces, _, _ = marching_cubes(mask, step_size=step_size)
return coords, faces
else:
return None, None
def add_trisurf(ax, arr, x, y, z, iso_val, **kwds):
verts, faces, normals, values = measure.marching_cubes(arr, iso_val)
verts_p = verts.copy()
verts_p[:, 2] = np.interp(verts_p[:, 2], np.arange(len(x)), x)
verts_p[:, 1] = np.interp(verts_p[:, 1], np.arange(len(y)), y)
verts_p[:, 0] = np.interp(verts_p[:, 0], np.arange(len(z)), z)
psurf = ax.plot_trisurf(verts_p[:, 2], verts_p[:, 1], faces, verts_p[:, 0],
**kwds)
return psurf
def three_d_print(volume_data):
b = raw_input('What resolution? (enter an int between 0 and 6, where 0 is highest resolution):\n')
name = raw_input('What should the filename be?') + '.stl'
verts, faces = measure.marching_cubes(volume_data, 0)
solid = mesh.Mesh(np.zeros(faces.shape[0], dtype=mesh.Mesh.dtype))
for i, f in enumerate(faces):
for j in range(3):
solid.vectors[i][j] = verts[f[j],:]
solid.save(name)
def isosurface(M,v,step,title=""):
"""
returns the isosurface of value v of M, subsetting M with the steps argument
"""
sel = np.arange(0,np.shape(M)[0],step)
verts, faces = measure.marching_cubes(M[np.ix_(sel,sel,sel)], v, spacing=(1.0, 1.0, 1.0))
fig = plt.figure(figsize = (10,7))
ax = fig.add_subplot(111, projection='3d')
ax.plot_trisurf(verts[:, 0], verts[:,1], faces, verts[:, 2], lw=.1, cmap="jet")
ax.axis("off")
ax.view_init(elev=35, azim=70)
plt.title(title)
plt.show()
def three_d_print(self):
"""This will produce a 3d printable stl based on self.volume_data. It is to be used for the final "print" button, and needs to be fed high quality data."""
name = raw_input('What should the filename be?') + '.stl'
verts, faces = measure.marching_cubes(self.volume_data, 0) #Marching Cubes algorithm
solid = mesh.Mesh(np.zeros(faces.shape[0], dtype=mesh.Mesh.dtype))
for i, f in enumerate(faces):
for j in range(3):
solid.vectors[i][j] = verts[f[j],:]
solid.save(name)
def marchingcubesobj(data,iso,objfile,scale=(1,1,1),center=(0,0,0),vertexoffset=0,excludeslice=False,debug=True):
if iso < data.min() or iso > data.max():
return 0,0
vert,face = measure.marching_cubes(data,iso)
vert[:,0]=scale[0]*(vert[:,0]-data.shape[0]/2.)+center[0]
vert[:,1]=scale[1]*(vert[:,1]-data.shape[1]/2.)+center[1]
vert[:,2]=scale[2]*(vert[:,2]-data.shape[2]/2.)+center[2]
if debug:
print 'Writing Data:'
for i in xrange(vert.shape[0]):
outstr = 'v %7.3f %7.3f %7.3f\n'%(vert[i,0],vert[i,1],vert[i,2])
objfile.write(outstr)
for i in xrange(face.shape[0]):
outstr = 'f %9d %9d %9d\n'%(face[i,0]+1+vertexoffset,face[i,1]+1+vertexoffset,face[i,2]+1+vertexoffset)
objfile.write(outstr)
# print (vert[:,0].min(),vert[:,1].min(),vert[:,2].min()),(vert[:,0].max(),vert[:,1].max(),vert[:,2].max())
return vert.shape[0], face.shape[0]
def visualize_voxel_spectral(points, vis_size=128):
"""Function to visualize voxel (spectral)."""
points = np.rint(points)
points = np.swapaxes(points, 0, 2)
fig = p.figure(figsize=(1, 1), dpi=vis_size)
verts, faces = measure.marching_cubes(points, 0, spacing=(0.1, 0.1, 0.1))
ax = fig.add_subplot(111, projection='3d')
ax.plot_trisurf(
verts[:, 0], verts[:, 1], faces, verts[:, 2], cmap='Spectral_r', lw=0.1)
ax.set_axis_off()
fig.tight_layout(pad=0)
fig.canvas.draw()
data = np.fromstring(
fig.canvas.tostring_rgb(), dtype=np.uint8, sep='').reshape(
vis_size, vis_size, 3)
p.close('all')
return data
def test_correct_mesh_orientation():
sphere_small = ellipsoid(1, 1, 1, levelset=True)
verts, faces = marching_cubes(sphere_small, 0.)
# Correct mesh orientation - descent
corrected_faces1 = correct_mesh_orientation(sphere_small, verts, faces,
gradient_direction='descent')
corrected_faces2 = correct_mesh_orientation(sphere_small, verts, faces,
gradient_direction='ascent')
# Ensure ascent is opposite of descent for all faces
np.testing.assert_array_equal(corrected_faces1, corrected_faces2[:, ::-1])
# Ensure correct faces have been reversed: 1, 4, and 5
idx = [1, 4, 5]
expected = faces.copy()
expected[idx] = expected[idx, ::-1]
np.testing.assert_array_equal(expected, corrected_faces1)
def implicit_surface(density_field,size,resolution,iso=0.5):
import numpy as np
from scipy.cluster.vq import kmeans, vq
from openalea.container import array_dict
from skimage.measure import marching_cubes
surface_points, surface_triangles = marching_cubes(density_field,iso)
surface_points = (np.array(surface_points))*(size*resolution/np.array(density_field.shape)) - size*resolution/2.
points_ids = np.arange(len(surface_points))
points_to_delete = []
for p,point in enumerate(surface_points):
matching_points = np.sort(np.where(vq(surface_points,np.array([point]))[1] == 0)[0])
if len(matching_points) > 1:
points_to_fuse = matching_points[1:]
for m_p in points_to_fuse:
surface_triangles[np.where(surface_triangles==m_p)] = matching_points[0]
points_to_delete.append(m_p)
points_to_delete = np.unique(points_to_delete)
print len(points_to_delete),"points deleted"
surface_points = np.delete(surface_points,points_to_delete,0)
points_ids = np.delete(points_ids,points_to_delete,0)
surface_triangles = array_dict(np.arange(len(surface_points)),points_ids).values(surface_triangles)
for p,point in enumerate(surface_points):
matching_points = np.where(vq(surface_points,np.array([point]))[1] == 0)[0]
if len(matching_points) > 1:
print p,point
raw_input()
triangles_to_delete = []
for t,triangle in enumerate(surface_triangles):
if len(np.unique(triangle)) < 3:
triangles_to_delete.append(t)
# elif triangle.max() >= len(surface_points):
# triangles_to_delete.append(t)
surface_triangles = np.delete(surface_triangles,triangles_to_delete,0)
return surface_points, surface_triangles
def marching_cubes(field,iso=0.5):
try:
from skimage.measure import marching_cubes
surface_points, surface_triangles = marching_cubes(density_field,iso)
except ImportError:
print "Please try to install SciKit-Image!"
from mayavi import mlab
from mayavi.mlab import contour3d
mlab.clf()
surface = mlab.contour3d(field,contours=[iso])
my_actor=surface.actor.actors[0]
poly_data_object=my_actor.mapper.input
surface_points = (np.array(poly_data_object.points) - np.array([abs(grid_points/2.),abs(grid_points/2.),abs(grid_points/2.)])[np.newaxis,:])*(grid_max/abs(grid_points/2.))
surface_triangles = poly_data_object.polys.data.to_array().reshape([-1,4])
surface_triangles = surface_triangles[:,1:]
return surface_points, surface_triangles
def plot_3d(image, threshold=-300):
# Position the scan upright,
# so the head of the patient would be at the top facing the camera
p = image.transpose(2,1,0)
verts, faces = measure.marching_cubes(p, threshold)
fig = plt.figure(figsize=(10, 10))
ax = fig.add_subplot(111, projection='3d')
# Fancy indexing: `verts[faces]` to generate a collection of triangles
mesh = Poly3DCollection(verts[faces], alpha=0.70)
face_color = [0.45, 0.45, 0.75]
mesh.set_facecolor(face_color)
ax.add_collection3d(mesh)
ax.set_xlim(0, p.shape[0])
ax.set_ylim(0, p.shape[1])
ax.set_zlim(0, p.shape[2])
plt.show()
def test_mc_skimage_orig_example(self):
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d.art3d import Poly3DCollection
from skimage import measure
from skimage.draw import ellipsoid
# Generate a level set about zero of two identical ellipsoids in 3D
ellip_base = ellipsoid(6, 10, 16, levelset=True)
ellip_double = np.concatenate((ellip_base[:-1, ...],
ellip_base[2:, ...]), axis=0)
# Use marching cubes to obtain the surface mesh of these ellipsoids
# outs = measure.marching_cubes(ellip_double, 0)
# verts, faces, normals, values = measure.marching_cubes(ellip_double, 0)
verts, faces = measure.marching_cubes(ellip_double, 0)
# Display resulting triangular mesh using Matplotlib. This can also be done
# with mayavi (see skimage.measure.marching_cubes docstring).
fig = plt.figure(figsize=(10, 10))
ax = fig.add_subplot(111, projection='3d')
# Fancy indexing: `verts[faces]` to generate a collection of triangles
mesh = Poly3DCollection(verts[faces])
mesh.set_edgecolor('k')
ax.add_collection3d(mesh)
ax.set_xlabel("x-axis: a = 6 per ellipsoid")
ax.set_ylabel("y-axis: b = 10")
ax.set_zlabel("z-axis: c = 16")
ax.set_xlim(0, 24) # a = 6 (times two for 2nd ellipsoid)
ax.set_ylim(0, 20) # b = 10
ax.set_zlim(0, 32) # c = 16
plt.tight_layout()
plt.show()
def plot_voxels(volume):
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d.art3d import Poly3DCollection
from skimage import measure
# Use marching cubes to obtain the surface mesh
verts, faces = measure.marching_cubes(volume, 0.5)
# Display resulting triangular mesh using Matplotlib. This can also be done
# with mayavi (see skimage.measure.marching_cubes docstring).
fig = plt.figure(figsize=(10, 12))
ax = fig.add_subplot(111, projection='3d')
# Fancy indexing: `verts[faces]` to generate a collection of triangles
mesh = Poly3DCollection(verts[faces])
ax.add_collection3d(mesh)
ax.set_xlim(0, volume.shape[0])
ax.set_ylim(0, volume.shape[1])
ax.set_zlim(0, volume.shape[2])
ax.set_aspect('equal')
plt.show()
def marche_cubes( ids , volume):
"""
Given a segmentation volume and set of ids,
it first computes a boolean volume, where every voxel
which correspond to an id present in the ids set is set to true.
It then create a mesh in the boundaries between true and false.
The generated mesh guarantees coherent orientation as of
version 0.12. of scikit-image
Args:
ids (tuple): segment ids that we want to generate a mesh from.
volume (numpy.array): volume to process
"""
shape = volume.shape
volume = np.in1d(volume,ids).reshape(shape)
try:
vertices, triangles = measure.marching_cubes(volume, 0.4)
except Exception, e:
return np.array([]), np.array([])
def isoSurface3d(image, level=1, fn='./plots/isosurf3d.html'): ''' wrapper function for plotly's isosurface 3d plots args: @a image: 3d array of numbers @a level: level at which to make an isocontour @a fn: string, filename to save plot as ''' vertices, simplices = measure.marching_cubes(image, level) x,y,z = zip(*vertices) fig = FF.create_trisurf( x=x, y=y, z=z, simplices=simplices ) py.offline.plot(fig, filename=fn)
def reconstruction_from2DtoSTL(path, name, way, size):
"""
Build a 3D object from a serie of 2D images.
Input parameters
----------------
path : str
Folder with 2D images.
name : str
Wanted name for the created STL file.
way : 'plot' or 'save'
Can plot the 3D object or can save it with the STL extension.
size : int or 'all'
Can have a 3D object with every face, or can have a divided 3D object.
Example : if size = 2, 1 of 2 slices on the x axis is taken,
1 of 2 slices on the y axis is taken,
and 1 of 2 slices on the z axis is taken,
so the 3D object is 8 times 'lighter'.
"""
plt.close('all')
line = currentframe().f_back.f_lineno
if path.__class__ != str:
print 'Line', line, '- Error: Directory must be str.'
exit()
elif name.__class__ != str:
print 'Line', line, '- Error: Name must be str.'
exit()
elif (way != 'plot' and way != 'save'):
print 'Line', line, '- Error: Way must be "plot" or "save".'
exit()
elif (size != 'all' and size.__class__ != int):
print 'Line', line, '- Error: Size must be "all" or int.'
exit()
else:
begin_time = time.time()
# pixel_file = (glob.glob(path.split(path.split('/')[-2])[0] + 'pixel_spacing.txt'))[0]
# with open(pixel_file, 'r') as pixel_readfile:
# for line in pixel_readfile:
# pixel_width = float(line.split('\t')[1])
# pixel_height = float(line.split('\t')[2])
# voxel_depth = float(line.split('\t')[3])$
pixel_width = 1.0
pixel_height = 1.0
voxel_depth = 1.0
files = glob.glob(path + '*')
files.sort()
# files.remove(pixel_file)
width = (misc.imread(files[0])).shape[0]
height = (misc.imread(files[0])).shape[1]
# width, height = (misc.imread(files[0])).shape
ZD_object = np.array([[0 for i in range(width)] for j in range(height)])
k = 1
for file in files:
try:
filename = file.split('/')[-1]
except:
filename = file.split('\\')[-1]
print 'Reading image', filename, '(', k, '/', str(len(files)), ')...'
image = misc.imread(file)
for i in range(width):
for j in range(height):
if len((image[i][j]).shape) != 0:
image[i][j] = image[i][j][0]
ZD_object = np.dstack((ZD_object, image))
k = k+1
append_time = time.time()
print 'Image reading and appending to 3D object time:', round(append_time - begin_time, 3), 'seconds'
print '\nSize of 3D object:', ZD_object.shape[0], 'x', ZD_object.shape[1], 'x', ZD_object.shape[2]
print '\nStarting the 3D reconstruction...'
if size == 'all':
verts, faces = measure.marching_cubes(ZD_object, 0.5, spacing = (pixel_width, pixel_height, voxel_depth))
else:
verts, faces = measure.marching_cubes(ZD_object[::size,::size,::size], 0.5, spacing = (pixel_width, pixel_height, voxel_depth))
marchingcubes_time = time.time()
print 'Marching cubes time:', round(marchingcubes_time - append_time, 3), 'seconds'
if way == 'plot':
print '\nPlotting the 3D object...'
fig = plt.figure(figsize=(10, 12))
ax = fig.add_subplot(111, projection='3d')
#ax = Axes3D(fig)
isosurface = Poly3DCollection(verts[faces])
ax.add_collection3d(isosurface)
ax.set_xlabel('x')
ax.set_ylabel('y')
ax.set_zlabel('z')
ax.set_xlim(0, 100)
ax.set_ylim(0, 100)
ax.set_zlim(0, 100)
plt.show()
plot_time = time.time()
print 'Plotting time:', round(plot_time - marchingcubes_time, 3), 'seconds'
elif way == 'save':
print '\nSaving the STL file...'
final_obj = mesh.Mesh(np.zeros(faces.shape[0], dtype=mesh.Mesh.dtype))
for i,f in enumerate(faces):
for j in range(3):
final_obj.vectors[i][j] = verts[f[j],:]
try:
path_1 = path.split(path.split('/')[-2])[0]
except:
path_1 = path.split(path.split('\\')[-2])[0]
final_obj.save(path_1 + name + '.stl')
save_time = time.time()
print 'Saving time:', round(save_time - marchingcubes_time, 3), 'seconds'
print '\n3D reconstruction done.\n'
dcm.append(os.path.join(filename))
#read first file to start array
ds = dicom.read_file(dcm[0])
ds1p = ds.pixel_array
dsfull = ds1p
for i in range(1,len(dcm)):
imgref = dcm[i]
ds = dicom.read_file(imgref)
pa = ds.pixel_array
dsfull = np.dstack((dsfull, pa))
dsfull = dsfull.swapaxes(0,2)
verts, faces = measure.marching_cubes(dsfull, 255)
fig = plt.figure(figsize=(692, 778))
ax = fig.add_subplot(111, projection='3d')
mesh = Poly3DCollection(verts[faces])
ax.add_collection3d(mesh)
ax.set_xlim(0, 21)
ax.set_ylim(0, 692)
ax.set_zlim(0, 778)
plt.show()
def plot_ellipsoid(self, hkle, dpi=100):
r"""Plots the resolution ellipsoid in the $Q_x$, $Q_y$, $W$ zone
Parameters
----------
hkle : tup
A tuple of intergers or arrays of H, K, L, and W (energy transfer)
values at which resolution ellipsoid are desired to be plotted
dpi : int, optional
Number of points in the plot
"""
try:
from skimage import measure
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
except ImportError:
raise
# clean arguments
[length, H, K, L, W] = _CleanArgs(*hkle)
# check if resolution already calculated at given hkle
try:
if np.all(H == self.H) and np.all(K == self.K) and np.all(L == self.L) and np.all(W == self.W):
NP = np.array(self.RMS)
R0 = self.R0
else:
self.calc_resolution(hkle)
NP = np.array(self.RMS)
R0 = self.R0
except AttributeError:
self.calc_resolution(hkle)
NP = np.array(self.RMS)
R0 = self.R0
if NP.shape == (4, 4):
NP = NP[np.newaxis]
R0 = [R0]
else:
NP = NP.T
# Create a canvas with a 3D viewport
fig = plt.figure(facecolor='w', edgecolor='k')
ax = fig.add_subplot(111, projection='3d')
for ind, (r0, rms) in enumerate(zip(R0, NP)):
qx0, qy0 = [np.dot([H[ind], K[ind], L[ind]], self.orient1 / np.linalg.norm(self.orient1) ** 2),
np.dot([H[ind], K[ind], L[ind]], self.orient2 / np.linalg.norm(self.orient2) ** 2)]
qw0 = W[ind]
def resolution_ellipsoid(prefac, resmat, x, y, w, x0, y0, w0):
r"""Resolution ellipsoid equation for qx, qy, and w dimensions
Parameters
----------
prefac : float
resmat : ndarray(4,4)
x : ndarray
y : ndarray
w : ndarray
x0 : float
y0 : float
w0 : float
Returns
-------
res_func : ndarray
"""
ee = (resmat[0, 0] * (x - x0) ** 2 +
resmat[1, 1] * (y - qy0) ** 2 +
resmat[3, 3] * (w - w0) ** 2 +
2 * resmat[0, 1] * (x - x0) * (y - y0) +
2 * resmat[0, 2] * (x - x0) * (w - w0) +
2 * resmat[1, 2] * (y - y0) * (w - w0))
return prefac * np.exp(-1 / 2 * ee)
# get fwhm to generate grid for plotting
w = []
for i in range(3):
_rms = np.delete(np.delete(rms, 2, axis=0), 2, axis=1)
w.append(fproject(_rms.reshape((3, 3, 1)), i)[0] * 1.01)
wx, wy, ww = w
# build grid
xg, yg, zg = np.mgrid[qx0 - wx:qx0 + wx:(dpi + 1) * 1j,
qy0 - wy:qy0 + wy:(dpi + 1) * 1j,
qw0 - ww:qw0 + ww:(dpi + 1) * 1j]
# resolution function (ellipsoidal gaussian)
vol = resolution_ellipsoid(r0, rms, xg, yg, zg, qx0, qy0, qw0)
# isosurface of resolution function at half-max
vertices, faces, normals, values = measure.marching_cubes(vol, vol.max() / 2.0, spacing=(wx / dpi, wy / dpi, ww / dpi))
# properly center ellipsoid
x_verts = vertices[:, 0] + qx0 - wx / 2
y_verts = vertices[:, 1] + qy0 - wy / 2
z_verts = vertices[:, 2] + qw0 - ww / 2
# plot ellipsoid
ax.plot_trisurf(x_verts, y_verts, faces, z_verts, lw=0, cmap='Spectral')
# figure labels
ax.ticklabel_format(style='plain', useOffset=False)
ax.set_xlabel(r'$q_x$ (along {0}) (r.l.u.)'.format(self.orient1), fontsize=12)
ax.set_ylabel(r'$q_y$ (along {0}) (r.l.u.)'.format(self.orient2), fontsize=12)
ax.set_zlabel(r'$\hbar \omega$ (meV)', fontsize=12)
plt.show()
"""
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d.art3d import Poly3DCollection
from skimage import measure
from skimage.draw import ellipsoid
# Generate a level set about zero of two identical ellipsoids in 3D
ellip_base = ellipsoid(6, 10, 16, levelset=True)
ellip_double = np.concatenate((ellip_base[:-1, ...],
ellip_base[2:, ...]), axis=0)
# Use marching cubes to obtain the surface mesh of these ellipsoids
verts, faces, normals, values = measure.marching_cubes(ellip_double, 0)
# Display resulting triangular mesh using Matplotlib. This can also be done
# with mayavi or visvis (see skimage.measure.marching_cubes docstring).
fig = plt.figure(figsize=(10, 12))
ax = fig.add_subplot(111, projection='3d')
# Fancy indexing: `verts[faces]` to generate a collection of triangles
mesh = Poly3DCollection(verts[faces])
ax.add_collection3d(mesh)
ax.set_xlabel("x-axis: a = 6 per ellipsoid")
ax.set_ylabel("y-axis: b = 10")
ax.set_zlabel("z-axis: c = 16")
ax.set_xlim(0, 24) # a = 6 (times two for 2nd ellipsoid)
print 'losses max -> ',(np.amax( losses ))
print 'losses argmax -> ',(np.argmax( losses ))
print 'losses x[max] -> ',g_x[(np.argmax( losses ))]
print 'v',v
print 'sigma',sigma
data = pop_data_grid(g_Desc[g_counter], g_Desc[g_counter].beta,g_Desc[g_counter].rho,
x0_max,x1_max,x2_max,x0_min,x1_min,x2_min)
proc_data(g_Desc[g_counter].beta,g_Desc[g_counter].rho,data)
# In[22]:
# Use marching cubes to obtain the surface mesh of these ellipsoids
verts, faces = measure.marching_cubes(data, 0)
for elev in [180,120,60,90]:
for azim in [30,90,180,240]:
# Display resulting triangular mesh using Matplotlib. This can also be done
# with mayavi (see skimage.measure.marching_cubes docstring).
fig = plt.figure(figsize=(10, 12))
ax = fig.add_subplot(111, projection='3d')
# Fancy indexing: `verts[faces]` to generate a collection of triangles
mesh = Poly3DCollection(verts[faces])
ax.add_collection3d(mesh)
ax.view_init(elev=elev, azim=azim)
ax.set_xlim(0,grid_steps)
ax.set_ylim(0,grid_steps)
def getVFByMarchingCubes(voxels, threshold=0.5):
v, f = sk.marching_cubes(voxels, level=threshold)
return v, f
def reconstruction_fromXYZtoSTL(file, way, size):
"""
Build a 3D object from a XYZ file.
Input parameters
----------------
file : str
XYZ file.
way : 'plot' or 'save'
Can plot the 3D object or can save it with the STL extension.
size : int or 'all'
Can have a 3D object with every face, or can have a divided 3D object.
Example : if size = 2, 1 of 2 slices on the x axis is taken,
1 of 2 slices on the y axis is taken,
and 1 of 2 slices on the z axis is taken,
so the 3D object is 8 times 'lighter'.
"""
line = currentframe().f_back.f_lineno
if file.__class__ != str:
print 'Line', line, '- Error: File must be str.'
exit()
elif (way != 'plot' and way != 'save'):
print 'Line', line, '- Error: Way must be "plot" or "save".'
exit()
elif (size != 'all' and size.__class__ != int):
print 'Line', line, '- Error: Size must be "all" or int.'
exit()
else:
begin_time = time.time()
print '\nStarting the conversion from a XYZ file to a STL file...'
images = reconstruction_fromXYZto2D(file, 'nosave')
XYZto2D_time = time.time()
print 'Converting from XYZ file to 2D images:', round(XYZto2D_time - begin_time, 3), 'seconds'
width = (images[0]).shape[0]
height = (images[0]).shape[1]
begin_time = time.time()
print "\nStarting the 3D reconstruction..."
ZD_object = np.array([[0 for i in range(width)] for j in range(height)])
for image in images:
ZD_object = np.dstack((ZD_object, image))
append_time = time.time()
print 'Image reading and appending to 3D object time:', round(append_time - XYZto2D_time, 3), 'seconds'
print '\nSize of 3D object:', ZD_object.shape[0], 'x', ZD_object.shape[1], 'x', ZD_object.shape[2]
if size == 'all':
verts, faces = measure.marching_cubes(ZD_object, 0.5)
else:
verts, faces = measure.marching_cubes(ZD_object[::size,::size,::size], 0.5)
marchingcubes_time = time.time()
print 'Marching cubes time:', round(marchingcubes_time - begin_time, 3), 'seconds'
if way == 'plot':
print '\nPlotting the 3D object...'
fig = plt.figure(figsize=(10, 12))
ax = fig.add_subplot(111, projection='3d')
#ax = Axes3D(fig)
isosurface = Poly3DCollection(verts[faces])
ax.add_collection3d(isosurface)
ax.set_xlabel('x')
ax.set_ylabel('y')
ax.set_zlabel('z')
ax.set_xlim(0, 100)
ax.set_ylim(0, 100)
ax.set_zlim(0, 100)
plt.show()
plot_time = time.time()
print 'Plotting time:', round(plot_time - marchingcubes_time, 3), 'seconds'
elif way == 'save':
print '\nSaving the STL file...'
final_obj = mesh.Mesh(np.zeros(faces.shape[0], dtype=mesh.Mesh.dtype))
for i,f in enumerate(faces):
for j in range(3):
final_obj.vectors[i][j] = verts[f[j],:]
name = file.split('.xyz')[0]
final_obj.save(name + '.stl')
save_time = time.time()
print 'Saving time:', round(save_time - marchingcubes_time, 3), 'seconds'
print '\n3D reconstruction done.\n'
def writeContoursToJson(LFP, x, y, z, n=1, directory='neuron'):
dname_base = 'contour_'
fname_base = 'frame_'
config_name = 'config.js'
dirs_config_name = 'contour_dir_list.js'
dx = np.abs(x[1] - x[0])
dy = np.abs(y[1] - y[0])
dz = np.abs(z[1] - z[0])
nx = len(x)
ny = len(y)
nz = len(z)
baseline = 0
# Choose n isopotentials between max amplitude and baseline, not
# including endpoints.
amp_max = LFP.max()
values_pos = []
if amp_max > 0:
values_pos = np.linspace(baseline, amp_max, n + 2)
values_pos = values_pos[1:-1]
amp_min = LFP.min()
values_neg = []
if amp_min < 0:
values_neg = np.linspace(baseline, amp_min, n + 2)
values_neg = values_neg[1:-1]
contour_directories = []
contour_cnt = 0
for iso_pot_val in values_pos:
# Create a seperate folder for each contour animation.
dir_name = dname_base + '%04d' % (contour_cnt)
contour_directories.append(dir_name)
dir_path = directory + '/' + dir_name
if not os.path.exists(dir_path):
os.makedirs(dir_path)
for i in xrange(LFP.shape[1]):
U = LFP[:, i].reshape(nx, ny, nz)
# The marching cubes algorithm cannot deal with levels
# outside the range of U.
if U.max() < iso_pot_val or U.min() > iso_pot_val:
verts = np.zeros([0, 3])
faces = np.zeros([0, 3])
else:
verts, faces = measure.marching_cubes(U,
iso_pot_val,
spacing=(dx, dy, dz))
verts[:, 0] = verts[:, 0] + x[0]
verts[:, 1] = verts[:, 1] + y[0]
verts[:, 2] = verts[:, 2] + z[0]
filename = fname_base + '%04d.js' % (i)
meshToJson(verts, faces, filename, dir_path)
# Save a config file listing all the data files.
data = {'n_frames': LFP.shape[1]}
dataString = json.dumps(data)
f = open(dir_path + '/' + config_name, 'w')
f.write(dataString)
f.close()
contour_cnt += 1
for iso_pot_val in values_neg:
# Create a seperate folder for each contour animation.
dir_name = dname_base + '%04d' % (contour_cnt)
contour_directories.append(dir_name)
dir_path = directory + '/' + dir_name
if not os.path.exists(dir_path):
os.makedirs(dir_path)
for i in xrange(LFP.shape[1]):
U = LFP[:, i].reshape(nx, ny, nz)
# The marching cubes algorithm cannot deal with levels
# outside the range of U.
if U.max() < iso_pot_val or U.min() > iso_pot_val:
verts = np.zeros([0, 3])
faces = np.zeros([0, 3])
else:
verts, faces = measure.marching_cubes(U,
iso_pot_val,
spacing=(dx, dy, dz))
verts[:, 0] = verts[:, 0] + x[0]
verts[:, 1] = verts[:, 1] + y[0]
verts[:, 2] = verts[:, 2] + z[0]
filename = fname_base + '%04d.js' % (i)
meshToJson(verts, faces, filename, dir_path)
# Save a config file listing all the data files.
data = {'n_frames': LFP.shape[1]}
dataString = json.dumps(data)
f = open(dir_path + '/' + config_name, 'w')
f.write(dataString)
f.close()
contour_cnt += 1
# Save a config file listing all the data files.
data = {'n_contours': len(contour_directories)}
dataString = json.dumps(data)
f = open(directory + '/' + dirs_config_name, 'w')
f.write(dataString)
f.close()
# get the error size
n_error_train = y_pred_train[y_pred_train == -1].size
# Distance of the samples X, Y, Z to the sperating hyperplane
Z = clf.decision_function(np.c_[xx.ravel(), yy.ravel(), zz.ravel()])
Z = Z.reshape(xx.shape)
plt.title("Novelty Detection")
ax = plt.gca(projection='3d')
# draw the points on the 3D graph
b1 = ax.scatter(X_train[:, 0], X_train[:, 1], X_train[:, 2], c='white')
# Signifies the Learning Curve
# IMP it should be better as the data set gets better
verts, faces = measure.marching_cubes(Z, 0)
verts = verts * \
[X_MAX - X_MIN, Y_MAX - Y_MIN, Z_MAX - Z_MIN] / SPACE_SAMPLING_POINTS
verts = verts + [X_MIN, Y_MIN, Z_MIN]
mesh = Poly3DCollection(verts[faces], facecolor='orange', edgecolor='gray', alpha=0.3)
ax.add_collection3d(mesh)
ax.set_xlim((-20, 20))
ax.set_ylim((-20, 20))
ax.set_zlim((-20, 20))
ax.axis('tight')
ax.set_xlabel("X")
ax.set_ylabel("Y")
ax.set_zlabel("Z")
# ax.legend([mpatches.Patch(color='orange', alpha=0.3), b1, b2, c],
phi = la.spsolve(K3, source3) phi = phi.reshape((N,N,N)) x = np.linspace(0,L,N,endpoint=False) y = np.linspace(0,L,N,endpoint=False) z = np.linspace(0,L,N,endpoint=False) xv, yv, zv = np.meshgrid(x,y,z) # http://scikit-image.org/docs/dev/auto_examples/plot_marching_cubes.html from skimage import measure verts, faces = measure.marching_cubes(phi, 0.01) #-.1 #print verts verts = verts * L / N # rescale verts from mpl_toolkits.mplot3d.art3d import Poly3DCollection import matplotlib.pyplot as plt from mpl_toolkits.mplot3d import Axes3D fig = plt.figure() ax = fig.add_subplot(111, projection='3d') mesh = Poly3DCollection(verts[faces]) ax.add_collection3d(mesh) verts, faces = measure.marching_cubes(phi, -0.01) #-.1
"""
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d.art3d import Poly3DCollection
from skimage import measure
from skimage.draw import ellipsoid
# Generate a level set about zero of two identical ellipsoids in 3D
ellip_base = ellipsoid(6, 10, 16, levelset=True)
ellip_double = np.concatenate((ellip_base[:-1, ...],
ellip_base[2:, ...]), axis=0)
# Use marching cubes to obtain the surface mesh of these ellipsoids
verts, faces = measure.marching_cubes(ellip_double, 0)
# Display resulting triangular mesh using Matplotlib. This can also be done
# with mayavi (see skimage.measure.marching_cubes docstring).
fig = plt.figure(figsize=(10, 12))
ax = fig.add_subplot(111, projection='3d')
# Fancy indexing: `verts[faces]` to generate a collection of triangles
mesh = Poly3DCollection(verts[faces])
ax.add_collection3d(mesh)
ax.set_xlabel("x-axis: a = 6 per ellipsoid")
ax.set_ylabel("y-axis: b = 10")
ax.set_zlabel("z-axis: c = 16")
ax.set_xlim(0, 24) # a = 6 (times two for 2nd ellipsoid)