def clust(elect_coords, n_clusts, iters, init_clusts):
# Load resultant coordinates from Hough circles transform
#coords = scipy.io.loadmat(elect_coords);
#dat = coords.get('elect_coords');
dat = elect_coords;
# Configure Kmeans
cluster = sklearn.cluster.KMeans();
cluster.n_clusters= n_clusts;
cluster.init = 'k-means++';
cluster.max_iter = iters;
cluster.verbose = 0;
cluster.n_init = init_clusts;
cluster.fit(dat);
# Grab vector for plotting each dimension
x = list(cluster.cluster_centers_[:,0]);
y = list(cluster.cluster_centers_[:,1]);
z = list(cluster.cluster_centers_[:,2]);
c = list(cluster.labels_);
scipy.io.savemat('k_labels.mat', {'labels':cluster.labels_})
scipy.io.savemat('k_coords.mat', {'coords':cluster.cluster_centers_})
# plot the results of kmeans
cmap = colors.Colormap('hot');
norm = colors.Normalize(vmin=1, vmax=10);
s = 64;
fig = plt.figure();
ax = fig.add_subplot(111,projection='3d');
Axes3D.scatter3D(ax,x,y,z,s=s);
plt.show(fig);
return cluster.cluster_centers_,cluster.labels_;
def elecDetect(CT_dir, T1_dir, img, thresh, frac, num_gridStrips, n_elects):
#navigate to dir with CT img
os.chdir(T1_dir)
# Extract and apply CT brain mask
mask_CTBrain(CT_dir, T1_dir, frac)
masked_img = 'masked_' + img
# run CT_electhresh
print "::: Thresholding CT at %f stdv :::" % (thresh)
electhresh(masked_img, thresh)
# run im_filt to gaussian smooth thresholded image
fname = "thresh_" + masked_img
print "::: Applying guassian smooth of 2.5mm to thresh-CT :::"
img_filt(fname)
# run hough transform to detect electrodes
new_fname = "smoothed_" + fname
print "::: Applying 2d Hough Transform to localize electrode clusts :::"
elect_coords = CT_hough(CT_dir, new_fname)
# set up x,y,z coords to view hough results
x = elect_coords[:, 0]
x = x.tolist()
y = elect_coords[:, 1]
y = y.tolist()
z = elect_coords[:, 2]
z = z.tolist()
# plot the hough results
s = 64
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
Axes3D.scatter3D(ax, x, y, z, s=s)
plt.show(fig)
# run K means to find grid and strip clusters
n_clusts = num_gridStrips
# number of cluster to find = number of electrodes
iters = 1000
init_clusts = n_clusts
print "::: Performing K-means cluster to find %d grid-strip and noise clusters :::" % (
n_clusts)
[clust_coords, clust_labels] = clust(elect_coords, n_clusts, iters,
init_clusts)
# run K means to find electrode center coordinates
n_clusts = n_elects
# number of cluster to find = number of electrodes
iters = 1000
init_clusts = n_clusts
print "::: Performing K-means cluster to find %d electrode centers :::" % (
n_clusts)
[center_coords, labels] = clust(elect_coords, n_clusts, iters, init_clusts)
print "::: Finished :::"
return elect_coords, clust_coords, clust_labels
def onpick(event):
# get event indices and x y z coord for click
ind = event.ind[0];
x_e, y_e, z_e = event.artist._offsets3d;
print x_e[ind], y_e[ind], z_e[ind];
seg_coord = [x_e[ind], y_e[ind], z_e[ind]];
seg_elecs.append(seg_coord);
# refresh plot with red dots picked and blue dots clean
#fig.clf();
seg_arr = np.array(seg_elecs);
x_f = seg_arr[:,0];
y_f = seg_arr[:,1];
z_f = seg_arr[:,2];
plt.cla();
Axes3D.scatter3D(ax,x_f,y_f,z_f,s=150,c='r', picker=5);
# get array of only clean elecs to re-plot as blue dots
clean_list = list(coords);
clean_list = [list(i) for i in clean_list];
for coordin in clean_list:
if list(coordin) in seg_elecs:
clean_list.pop(clean_list.index(coordin));
clean_coordis = np.array(clean_list);
x_c = clean_coordis[:,0];
y_c = clean_coordis[:,1];
z_c = clean_coordis[:,2];
Axes3D.scatter3D(ax,x_c, y_c, z_c, s=150,c='b', picker=5);
time.sleep(0.5);
plt.draw();
def onpick(event):
# get event indices and x y z coord for click
ind = event.ind[0];
x_e, y_e, z_e = event.artist._offsets3d;
print x_e[ind], y_e[ind], z_e[ind];
seg_coord = [x_e[ind], y_e[ind], z_e[ind]];
seg_elecs.append(seg_coord);
# refresh plot with red dots picked and blue dots clean
#fig.clf();
seg_arr = np.array(seg_elecs);
x_f = seg_arr[:,0];
y_f = seg_arr[:,1];
z_f = seg_arr[:,2];
plt.cla();
Axes3D.scatter3D(ax,x_f,y_f,z_f,s=150,c='r', picker=5);
# get array of only clean elecs to re-plot as blue dots
clean_list = list(coords);
clean_list = [list(i) for i in clean_list];
for coordin in clean_list:
if list(coordin) in seg_elecs:
clean_list.pop(clean_list.index(coordin));
clean_coordis = np.array(clean_list);
x_c = clean_coordis[:,0];
y_c = clean_coordis[:,1];
z_c = clean_coordis[:,2];
Axes3D.scatter3D(ax,x_c, y_c, z_c, s=150,c='b', picker=5);
time.sleep(0.5);
plt.draw();
def clust(elect_coords, n_clusts, iters, init_clusts):
# Load resultant coordinates from Hough circles transform
#coords = scipy.io.loadmat(elect_coords);
#dat = coords.get('elect_coords');
dat = elect_coords
# Configure Kmeans
cluster = sklearn.cluster.KMeans()
cluster.n_clusters = n_clusts
cluster.init = 'k-means++'
cluster.max_iter = iters
cluster.verbose = 0
cluster.n_init = init_clusts
cluster.fit(dat)
# Grab vector for plotting each dimension
x = list(cluster.cluster_centers_[:, 0])
y = list(cluster.cluster_centers_[:, 1])
z = list(cluster.cluster_centers_[:, 2])
c = list(cluster.labels_)
scipy.io.savemat('k_labels.mat', {'labels': cluster.labels_})
scipy.io.savemat('k_coords.mat', {'coords': cluster.cluster_centers_})
# plot the results of kmeans
cmap = colors.Colormap('hot')
norm = colors.Normalize(vmin=1, vmax=10)
s = 64
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
Axes3D.scatter3D(ax, x, y, z, s=s)
plt.show(fig)
return cluster.cluster_centers_, cluster.labels_
def elecDetect(CT_dir, T1_dir, img, thresh, frac, num_gridStrips, n_elects):
# navigate to dir with CT img
os.chdir(T1_dir)
# Extract and apply CT brain mask
mask_CTBrain(CT_dir, T1_dir, frac)
masked_img = "masked_" + img
# run CT_electhresh
print "::: Thresholding CT at %f stdv :::" % (thresh)
electhresh(masked_img, thresh)
# run im_filt to gaussian smooth thresholded image
fname = "thresh_" + masked_img
print "::: Applying guassian smooth of 2.5mm to thresh-CT :::"
img_filt(fname)
# run hough transform to detect electrodes
new_fname = "smoothed_" + fname
print "::: Applying 2d Hough Transform to localize electrode clusts :::"
elect_coords = CT_hough(CT_dir, new_fname)
# set up x,y,z coords to view hough results
x = elect_coords[:, 0]
x = x.tolist()
y = elect_coords[:, 1]
y = y.tolist()
z = elect_coords[:, 2]
z = z.tolist()
# plot the hough results
s = 64
fig = plt.figure()
ax = fig.add_subplot(111, projection="3d")
Axes3D.scatter3D(ax, x, y, z, s=s)
plt.show(fig)
# run K means to find grid and strip clusters
n_clusts = num_gridStrips
# number of cluster to find = number of electrodes
iters = 1000
init_clusts = n_clusts
print "::: Performing K-means cluster to find %d grid-strip and noise clusters :::" % (n_clusts)
[clust_coords, clust_labels] = clust(elect_coords, n_clusts, iters, init_clusts)
# run K means to find electrode center coordinates
n_clusts = n_elects
# number of cluster to find = number of electrodes
iters = 1000
init_clusts = n_clusts
print "::: Performing K-means cluster to find %d electrode centers :::" % (n_clusts)
[center_coords, labels] = clust(elect_coords, n_clusts, iters, init_clusts)
print "::: Finished :::"
return elect_coords, clust_coords, clust_labels
def plot(self, ax: Axes3D, obj: Object, zorder: int = 1) -> Axes3D:
assert obj.points is not None
ax.scatter3D(obj.points[:, 0],
obj.points[:, 1],
obj.points[:, 2],
c=obj.points[:, 2],
cmap=obj.cmap,
edgecolors=obj.edgecolors,
linewidths=obj.linewidths,
s=obj.markersize)
return ax
def quick_plot_3D(
ct_data,
ax: Axes3D = None,
step_size: int = 50,
is_long: bool = False,
is_norm: bool = False,
base_color: Tuple = (0, 0, 0),
alpha_max: float = 1.0,
):
""" Plots subsampled CT/MRI data
Arguments:
ct_data {Nibabel object data} -- Data from a nibabel object using the .get_fdata() method
to shorten compute time, send the voxel_to_4D output and set the is_long variable to True.
Keyword Arguments:
step_size {int} -- sample step size
For example this function defaults to 1 point in 50 (default: {50})
is_long {bool} -- set if precomputed 4D vector array using voxels_to_4D, shortens computation
is_norm {bool} -- set if data is already normalized from 0 to 1 (default: False)
base_color {Tuple} -- three value'd tuple of RGB values
alpha_max {float} -- value between 0 and 1 for transparancy
"""
if not is_long:
long_data = rd.voxels_to_4D(ct_data, is_norm)
else:
long_data = ct_data
if is_norm:
vals = long_data[::step_size, 3]
else:
vals = fct.min_max_normalize(long_data[::step_size, 3])
if ax is None:
fig = plt.figure(figsize=(16, 16))
ax = fig.add_subplot(111, projection='3d')
colors = [(base_color[0], base_color[1], base_color[2], n * alpha_max)
for n in vals]
ax.scatter3D(long_data[::step_size, 0],
long_data[::step_size, 1],
long_data[::step_size, 2],
c=colors)
return ax
# repeat for center img data
img_data = scipy.io.loadmat('elec_centers.mat')
img_data = img_data.get('center_img')
new_fname = 'CT_elecCenters.nii'
N = nib.Nifti1Image(img_data, affine, hdr)
N.to_filename(new_fname)
# get img dims
z_len = img_data[0, 0, :].shape
x_len = img_data[:, 0, 0].shape
y_len = img_data[0, :, 0].shape
# get coords of voxels containing center data
coords = np.nonzero(img_data)
x = coords[0]
y = coords[1]
z = coords[2]
# concatonate xyz vectors into 3 x n matrix
stackem = (x, y, z)
coords = np.vstack(stackem)
coords = np.transpose(coords)
scipy.io.savemat('3dcv_coords.mat', {'coords': coords})
# plot the cv center results
s = 202
fig = plt.figure(facecolor="white")
ax = fig.add_subplot(111, projection='3d')
Axes3D.scatter3D(ax, x, y, z, s=s)
plt.show(fig)
def seg_3D(CT_dir,fname, out_fname):
# load in 3D output
coords = scipy.io.loadmat(CT_dir + '/' + fname).get('elecmatrix');
x = coords[:,0];
y = coords[:,1];
z = coords[:,2];
# plot dirty elec results
s = 150;
fig = plt.figure(facecolor="white");
ax = fig.add_subplot(111,projection='3d');
# create point and click function for selecting false alarm points
seg_elecs = [];
def onpick(event):
# get event indices and x y z coord for click
ind = event.ind[0];
x_e, y_e, z_e = event.artist._offsets3d;
print x_e[ind], y_e[ind], z_e[ind];
seg_coord = [x_e[ind], y_e[ind], z_e[ind]];
seg_elecs.append(seg_coord);
# refresh plot with red dots picked and blue dots clean
#fig.clf();
seg_arr = np.array(seg_elecs);
x_f = seg_arr[:,0];
y_f = seg_arr[:,1];
z_f = seg_arr[:,2];
plt.cla();
Axes3D.scatter3D(ax,x_f,y_f,z_f,s=150,c='r', picker=5);
# get array of only clean elecs to re-plot as blue dots
clean_list = list(coords);
clean_list = [list(i) for i in clean_list];
for coordin in clean_list:
if list(coordin) in seg_elecs:
clean_list.pop(clean_list.index(coordin));
clean_coordis = np.array(clean_list);
x_c = clean_coordis[:,0];
y_c = clean_coordis[:,1];
z_c = clean_coordis[:,2];
Axes3D.scatter3D(ax,x_c, y_c, z_c, s=150,c='b', picker=5);
time.sleep(0.5);
plt.draw();
Axes3D.scatter3D(ax,x,y,z,s=s, picker=5);
#title_font = {'fontname':'serif', 'size':'24', 'color':'black', 'weight':'bold',
#'verticalalignment':'bottom'};
plt.title('3D Output Coordinates: ');
fig.canvas.mpl_connect('pick_event', onpick);
plt.ion();
plt.show(fig);
# wait for user to press enter to continue
while True:
fig.canvas.mpl_connect('pick_event', onpick);
plt.draw();
i = raw_input("Enter text or Enter to quit: ");
if i == '':
# remove all false coords from elec centers list
fig.clf();
coords_list = list(coords);
coords_list = [list(i) for i in coords_list];
for coordi in coords_list:
if list(coordi) in seg_elecs:
coords_list.pop(coords_list.index(coordi));
clean_coords = np.array(seg_elecs)
# plot result
X = clean_coords[:,0];
Y = clean_coords[:,1];
Z = clean_coords[:,2];
s = 150;
fig = plt.figure(facecolor="white");
ax = fig.add_subplot(111,projection='3d');
Axes3D.scatter3D(ax,X,Y,Z,s=s);
plt.show(fig);
# save the cleaned elecs file
new_fname = CT_dir + '/' + out_fname;
scipy.io.savemat(new_fname, {'elecmatrix':clean_coords});
return clean_coords;
break;
def seg_Hough3D(CT_dir,fname, out_fname):
# load in 3D hough output
coords = scipy.io.loadmat(CT_dir + '/' + fname).get('elecmatrix');
x = coords[:,0];
y = coords[:,1];
z = coords[:,2];
# plot dirty elec results
s = 150;
fig = plt.figure(facecolor="white");
ax = fig.add_subplot(111,projection='3d');
# create point and click function for selecting false alarm points
seg_elecs = [];
def onpick(event):
# get event indices and x y z coord for click
ind = event.ind[0];
x_e, y_e, z_e = event.artist._offsets3d;
print x_e[ind], y_e[ind], z_e[ind];
seg_coord = [x_e[ind], y_e[ind], z_e[ind]];
seg_elecs.append(seg_coord);
# refresh plot with red dots picked and blue dots clean
#fig.clf();
seg_arr = np.array(seg_elecs);
x_f = seg_arr[:,0];
y_f = seg_arr[:,1];
z_f = seg_arr[:,2];
plt.cla();
Axes3D.scatter3D(ax,x_f,y_f,z_f,s=150,c='r', picker=5);
# get array of only clean elecs to re-plot as blue dots
clean_list = list(coords);
clean_list = [list(i) for i in clean_list];
for coordin in clean_list:
if list(coordin) in seg_elecs:
clean_list.pop(clean_list.index(coordin));
clean_coordis = np.array(clean_list);
x_c = clean_coordis[:,0];
y_c = clean_coordis[:,1];
z_c = clean_coordis[:,2];
Axes3D.scatter3D(ax,x_c, y_c, z_c, s=150,c='b', picker=5);
time.sleep(0.5);
plt.draw();
Axes3D.scatter3D(ax,x,y,z,s=s, picker=5);
#title_font = {'fontname':'serif', 'size':'24', 'color':'black', 'weight':'bold',
#'verticalalignment':'bottom'};
plt.title('Hough 3D Output Coordinates: ');
fig.canvas.mpl_connect('pick_event', onpick);
plt.ion();
plt.show(fig);
# wait for user to press enter to continue
while True:
fig.canvas.mpl_connect('pick_event', onpick);
plt.draw();
i = raw_input("Enter text or Enter to quit: ");
if i == '':
# remove all false coords from elec centers list
fig.clf();
coords_list = list(coords);
coords_list = [list(i) for i in coords_list];
for coordi in coords_list:
if list(coordi) in seg_elecs:
coords_list.pop(coords_list.index(coordi));
clean_coords = np.array(seg_elecs)
# plot result
X = clean_coords[:,0];
Y = clean_coords[:,1];
Z = clean_coords[:,2];
s = 150;
fig = plt.figure(facecolor="white");
ax = fig.add_subplot(111,projection='3d');
Axes3D.scatter3D(ax,X,Y,Z,s=s);
plt.show(fig);
# save the cleaned elecs file
new_fname = CT_dir + '/' + out_fname;
scipy.io.savemat(new_fname, {'elecmatrix':clean_coords});
return clean_coords;
break;
# get img dims
z_len = img_data[0,0,:].shape;
x_len = img_data[:,0,0].shape;
y_len = img_data[0,:,0].shape;
# get coords of voxels containing center data
coords = np.nonzero(img_data);
x = coords[0];
y = coords[1];
z = coords[2];
# concatonate xyz vectors into 3 x n matrix
stackem = (x,y,z);
coords = np.vstack(stackem);
coords = np.transpose(coords);
scipy.io.savemat('3dHough_coords.mat', {'coords':coords});
# plot the hough center results
s = 202
fig = plt.figure(facecolor="white");
ax = fig.add_subplot(111,projection='3d');
Axes3D.scatter3D(ax,x,y,z,s=s);
plt.show(fig);
de1 = math.sqrt(de / len(x))
return de1
print('Percentage Error: ', percent_error())
# surface data
fig = plt.figure()
# Red is the spline and Blue is the smooth_path.csv
ax = fig.add_subplot(111, projection='3d')
Axes3D.plot(ax, xs=x, ys=y, zs=z, color='red')
Axes3D.plot(ax, xs=x_axis, ys=y_axis, zs=z_axis, color='blue')
# Purple is the control points
Axes3D.scatter3D(ax,
xs=control_vector_x,
ys=control_vector_y,
zs=control_vector_z,
s=0.25,
color='purple')
plt.show()
# s contains all the radius data
# tube radius is varied by a factor 0.1 * radius for a cleaner 3D output
s = radius_data / 2
user_using = True
while user_using == True:
# User input for vessel representation
print()
print('Vessel representations:')
print('[1]: Given Smooth Path')
print('[2]: B-Spline Values')
