alina.py

import pytrip as pt

# first define some paths and other important parameters
ctx_path = "tests/sphere000.ctx"
vdx_path = "tests/sphere000.vdx"
my_target_voi = "bsPTVClassic0"

# load CT cube
my_ctx = pt.CtxCube()
my_ctx.read(ctx_path)

print(my_ctx.cube.min(), my_ctx.cube.max() )

# load VOIs
my_vdx = pt.VdxCube("", my_ctx)  # my_vdx is the object which will hold all volumes of interest and the meta information
my_vdx.read(vdx_path)  # load the .vdx file
print(my_vdx.get_voi_names())  # show us all VOIs found in the .vdx file

# Select the requested VOI from the VdxCube object
target_voi = my_vdx.get_voi_by_name(my_target_voi)

print("X max", my_ctx.pixel_size * my_ctx.dimx)
print("Y max", my_ctx.pixel_size * my_ctx.dimy)
print("Z max", my_ctx.slice_distance * my_ctx.dimz)

# get_voi_cube() returns a DosCube() object, where all voxels inside the VOI holds the value 1000, and 0 elsewhere.
voi_cube = target_voi.get_voi_cube()

for k,slice in target_voi.slices.items():
    print("slice no", k, slice)
    for c in slice.contour:
        print("c", c)
        for c2 in c.contour:
            print("c2", c2)

print("vc", voi_cube.cube.min(), voi_cube.cube.max())

# Based on the retrieved DosCube() we calculate a three dimensional mask object,
# which assigns True to all voxels inside the Voi, and False elsewhere.
mask = (voi_cube.cube == 1000)

# "The mask object and the CTX cube have same dimensions (they are infact inherited from the same top level class).
# Therefore we can apply the mask cube to the ctx cube and work with the values.
# For instance we can set all HUs to zero within the Voi:
my_ctx.cube[mask] = -1000
# or add 100 to all HUs of the voxels inside the mask:
# my_ctx.cube[mask] += 100

# save masked CT to the file in current directory
masked_ctx = "masked.ctx"
my_ctx.write(masked_ctx)

print(my_ctx.cube.max(), my_ctx.cube.min())