def visualizeTraj(postSurfImgFp, vesselImgFp, ventricleImgFp, brainSurfImgFp, ANTImgFp, startingPt, targetPt, saveDir):
postSurf = utils.readImg(postSurfImgFp)
dist = ((targetPt[0] - startingPt[0]) ** 2 + (targetPt[1] - startingPt[1]) ** 2
+ (targetPt[2] - startingPt[2]) ** 2) ** 0.5
flow = [(targetPt[0] - startingPt[0]) / dist, (targetPt[1] - startingPt[1]) / dist,
(targetPt[2] - startingPt[2]) / dist]
traj = np.zeros(postSurf.shape)
nPt = int(dist)
print(f"Direction of the trajectory: ", flow)
print(f"Number of points: ", nPt)
print("** Generating the trajectory **")
for idx in range(nPt):
x = int(round(startingPt[1] + flow[1] * idx))
y = int(round(startingPt[0] + flow[0] * idx))
z = int(round(startingPt[2] + flow[2] * idx))
traj[x, y, z] = 1
# extend the trajectory
for idx in range(25):
x = int(round(startingPt[1] - flow[1] * idx))
y = int(round(startingPt[0] - flow[0] * idx))
z = int(round(startingPt[2] - flow[2] * idx))
traj[x, y, z] = 1
traj = scipy.ndimage.morphology.binary_dilation(traj)
traj = traj.astype(dtype="uint16")
# plot the target point
target = np.zeros(postSurf.shape)
target[targetPt[1]-2:targetPt[1]+2, targetPt[0]-2:targetPt[0]+2, targetPt[2]-2:targetPt[2]+2] = 1
# include other components in our window
vessel = utils.readImg(vesselImgFp)
ventricle = utils.readImg(ventricleImgFp)
brain = utils.readImg(brainSurfImgFp)
ANT = utils.readImg(ANTImgFp)
# Assign with different colors
traj[np.where(traj != 0)] = 2000 # trajectory
ventricle[np.where(ventricle != 0)] = 20 # ventricles
postSurf[np.where(postSurf != 0)] = 10 # post-surface
brain[np.where(brain != 0)] = 5 # brain-surface
vessel[np.where(vessel != 0)] = 200 # vessel
target[np.where(target != 0)] = 50 # target point
ANT[np.where(ANT != 0)] = 300 # ANT
# plot the final planning graph
finalPlanning = ventricle + postSurf + traj + vessel + brain + ANT # + target
finalPlanning[np.where(finalPlanning == 15)] = 10
finalPlanning[np.where(finalPlanning == 210)] = 10
finalPlanning[np.where(finalPlanning == 215)] = 10
finalPlanning[np.where(finalPlanning == 2000)] = 2005
finalPlanning[np.where(finalPlanning == 2015)] = 2005
finalPlanning = finalPlanning.astype(dtype="uint16")
utils.saveImg(finalPlanning, saveDir+"/final_planning.nii")
return finalPlanning
def generateSurf(targetSurfImgFp, saveDir):
img = utils.readImg(targetSurfImgFp)
img = scipy.ndimage.morphology.binary_dilation(img)
surf = np.zeros(img.shape)
for x in range(60, 117):
for y in range(176):
# from superior to inferior
for z in range(100,176)[::-1]:
if img[x, y, z] == 1:
surf[x, y, z] = 1
break
for x in range(60, 117):
for z in range(100, 176):
# from right to left
for y in range(176)[::-1]:
if img[x, y, z] == 1:
surf[x, y, z] = 1
break
# from left to right
for y in range(176):
if img[x, y, z] == 1:
surf[x, y, z] = 1
break
# for y in range(176):
# for z in range(100, 176):
# # from anterior to posterior
# for x in range(60, 117):
# if img[x, y, z] == 1:
# surf[x, y, z] = 1
# break
surf = surf.astype(dtype="uint16")
utils.saveImg(surf, saveDir+"/surface.nii")
return surf
def openVideo(self, img_dir, n_frame=None):
self.vid_opened = True
self.images = utils.readImg(img_dir)
width = self.vid_player.width()
height = self.vid_player.height()
img = self.image_holder.setup(self.images, width, height, colour=self.user["Colour"], n_frame=n_frame)
self.changeFrameTo(img)
def skullStrip(imgFp, saveDir):
img = utils.readImg(imgFp)
ext = Extractor()
prob = ext.run(img)
mask = (prob > 0.5)
mask = mask.astype(dtype="uint16")
utils.saveImg(mask, saveDir + "/skull-strip.nii")
return mask
def fetchData(data_frame, batch_cache):
df = self.data_frame.iloc(batch_cache).reset_index(drop=True)
images = []
for img_file in df[0].values:
img = np.asarray(utils.readImg(img_file))
if len(img.shape) == 2:
img.resize(img.shape[0], img.shape[1], 1)
images.append(img)
labels = df[1].values
return images, labels
def generateTargetSurf(brainSurfImgFp, saveDir):
img = utils.readImg(brainSurfImgFp)
for x in range(256): # Anterior-Posterior
for y in range(176): # Left-Right
for z in range(176): # Superior-Inferior
# define the boundaries of x, y and z
if x < 60 or x > 117 or z < 100:
img[x, y, z] = 0
img = img.astype(dtype="uint16")
utils.saveImg(img, saveDir + "/target-surf.nii")
return img
def generateBrainSurf(rawImgFp, saveDir, thresh=15):
img = utils.readImg(rawImgFp)
img[np.where(img < thresh)] = 0 # global threshold
img = scipy.ndimage.morphology.binary_erosion(img) # erosion
img = utils.getLargestConnectedComp(img) # largest connected component
img = scipy.ndimage.morphology.binary_dilation(img) # dilation
# eliminate the outlier
for y in range(14):
for z in range(114, 119):
for x in range(256):
img[x, y, z] = 0
img = img.astype(dtype="uint16")
utils.saveImg(img, saveDir + "/brain-surf.nii")
return img
def generateSegFromSlant(slantMskFp, saveDir):
# SLANT segmentation labels:
# 59: Right thalamus
# 60: Left thalamus
# 4: 3rd ventricle
# 11: 4th ventricle
# 51: Right Lateral Ventricle # 52: Left Lateral Ventricle
names = ["right-thalamus", "left-thalamus", "3rd-ventricle", "4th-ventricle", "RLV", "LLV"]
for i, label in enumerate([59, 60, 4, 11, 51, 52]):
msk = utils.readImg(slantMskFp)
msk[np.where(msk != label)] = 0
msk[np.where(msk != 0)] = 1
msk = msk.astype(dtype="uint16")
utils.saveImg(msk, saveDir+"/Normal003-"+names[i]+".nii")
def fillSurf(targetSurfImgFp, saveDir):
img = utils.readImg(targetSurfImgFp)
for y in range(176):
for x in range(60, 117):
top = 0
for z in range(100, 176)[::-1]:
if img[x, y, z] == 1:
top = z
break
for z in range(100, top):
img[x, y, z] = 1
img = scipy.ndimage.morphology.binary_dilation(img)
img = img.astype(dtype="uint16")
utils.saveImg(img, saveDir + "/fill-surf.nii")
return img
def postProcessSurf(surfImgFp, saveDir):
img = utils.readImg(surfImgFp)
img = scipy.ndimage.morphology.binary_dilation(img)
img = img.astype(dtype="uint16")
utils.saveImg(img, saveDir + "/post-surface.nii")
return img