Hi Chiara,
Can you test this?
import imfusion as imf
import imfusion.ultrasound as us
import numpy as np
def sliceSizeFromGeometry(frameGeometry):
if frameGeometry.is_linear:
extent = [frameGeometry.img_desc.width / 2.0, frameGeometry.img_desc.depth / 2.0]
elif frameGeometry.is_convex:
sx = 2 * frameGeometry.long_radius * np.sin(np.deg2rad(frameGeometry.opening_angle))
sy = frameGeometry.long_radius - frameGeometry.short_radius * np.cos(np.deg2rad(frameGeometry.opening_angle))
extent = [sx.item(), sy.item()]
return extent;
def createConvexGeometry(probe_width, long_radius, depth, opening_angle):
# Set up the desired frame geometry for the ultrasound sweep:
fg = us.FrameGeometryConvex(us.CoordinateSystem.IMAGE)
# The sweep requires a valid image descriptor for the frame geometry
fg.img_desc = imf.ImageDescriptor(imf.PixelType.UBYTE,128,128,1,1)
# Set up the frame geometry dimensions:
fg.opening_angle = opening_angle
fg.short_radius = probe_width / (2 * np.sin(np.deg2rad(opening_angle))).item()
fg.long_radius = long_radius
fg.depth = depth
fg.top_down = True
return fg
def createLinearGeometry(probe_width, depth, opening_angle):
# Set up the desired frame geometry for the ultrasound sweep:
fg = us.FrameGeometryLinear(us.CoordinateSystem.IMAGE)
# The sweep requires a valid image descriptor for the frame geometry
fg.img_desc = imf.ImageDescriptor(imf.PixelType.UBYTE,128,128,1,1)
# Set up the frame geometry dimensions:
fg.width = probe_width
fg.depth = depth
fg.top_down = True
return fg
def setCenter(fg, extent):
# Probe center is horizontally centered
if fg.is_convex:
sign = 1 if fg.top_down else 0
y = -extent[0] + sign * fg.short_radius * (1 - np.cos(np.deg2rad(fg.opening_angle))).item();
fg.offset = np.array([0,y])
if fg.is_linear:
fg.offset = np.array([0,-extent[1]])
def createEmptyImage(extent):
img_desc = imf.ImageDescriptor(imf.PixelType.UBYTE,128,128,1,1)
img_desc.spacing = np.array([extent[0] * 2 / 128, extent[1] * 2 / 128,1])
img_desc.is_metric = True
im = imf.SharedImage(imf.MemImage(img_desc))
return im
# Retrieve the tracking from the suite data model
trackings = [el for el in imf.app.data_model if type(el) == imf.TrackingSequence]
if len(trackings) == 0:
print("Error, no trackings found in the data model")
tracking = trackings[0]
# Generate a sweep
sweep = us.UltrasoundSweep()
sweep.name = "Synthetic Sweep from csv poses"
# Add an empty image to the sweep for every position in the tracking
# Create a copy
tracking_copy = imf.TrackingSequence()
opening_angle = 30
short_radius = 0
long_radius = 100
depth = 50
top_down = True
fg = createConvexGeometry(short_radius, long_radius, depth, opening_angle)
extent = sliceSizeFromGeometry(fg)
setCenter(fg,extent)
# Duration of the sweep, in seconds
sweep_time = 3
nframes = tracking.size
timestep = sweep_time / (nframes - 1)
perpendicularSlices = True
for i in range(1,nframes-1):
m = tracking.raw_matrix(i)
t = i * timestep
# Vector of sensor pointing
d = np.array([0,-60,0])
depth_axis = d / np.linalg.norm(d)
# Very simple tangent computation without splines
sweep_tangent = tracking.raw_matrix(i+1)[:3,3] - tracking.raw_matrix(i-1)[:3,3]
sweep_tangent /= np.linalg.norm(sweep_tangent)
normalSlice = np.cross(sweep_tangent, depth_axis)
if(perpendicularSlices):
normalSlice = np.cross(depth_axis,normalSlice)
outMat = np.eye(4)
outMat[:3,0] = np.cross(depth_axis,normalSlice)
outMat[:3,1] = depth_axis
outMat[:3,2] = normalSlice
outMat[:3,3] = m[:3,3] + (depth_axis * extent[1])
print(outMat)
tracking_copy.add(outMat,t,1.0)
sweep.add(createEmptyImage(extent))
sweep.set_timestamp(t,i)
# Add the tracking
sweep.add_tracking(tracking_copy)
sweep.properties.set_param("topDown", True)
# Change this sweep frame geometry through its metadata component
fgm = [el for el in sweep.components if type(el) == us.FrameGeometryMetadata][0]
fgm.frame_geometry = fg
# Add to the data model
imf.app.data_model.add(sweep)
Run it on the suite python console and it will generate a sweep with garbage image data with the positions from the tracking sequence. You can use this sweep for running the simulation. I put a [0,-60,0] difference between the transducer and direction from the workspace file you shared. If you want a custom direction of scanning or use the ones in the tracking sequence you’ll have to redo the maths for the outMat at the end. For other geometries you’ll have to fill in the if cases, I think they are straight forward but if you need help do not hesitate to ask.
Have a great weekend!
Alejandro
