MergeAdjacentImages Notebook

This notebook contains a few examples of how to use the MergeAdjacentImages application from TubeTK. First, we will include Python's os package as well as SimpleITK (Python wrapping). We also set the TubeTK build directory variable TUBETK_BUILD_DIR:

In [6]:
import os
import sys
import SimpleITK as sitk
import matplotlib.pyplot as plt
from matplotlib import cm

TubeTK_BINARY_DIR = None
if 'TubeTK_BINARY_DIR' in os.environ:
    TubeTK_BINARY_DIR = os.environ['TubeTK_BINARY_DIR']
elif len(sys.argv) > 1:
    TubeTK_BINARY_DIR = sys.argv[1]

if not os.path.exists(TubeTK_BINARY_DIR):
    print('TubeTK_BINARY_DIR not found!')
    sys.exit(1)
An exception has occurred, use %tb to see the full traceback.

SystemExit: 1
TubeTK_BINARY_DIR not found!

To exit: use 'exit', 'quit', or Ctrl-D.

Next, we load the first input image and show it's origin, spacing, etc.:

In [5]:
input_image1 = os.path.join(TubeTK_BINARY_DIR, 'MIDAS_Data/ES0015_Large.mha')
im0 = sitk.ReadImage(input_image1)
print im0.GetOrigin()
print im0.GetSpacing()
print im0.GetDirection()
(200.0, 200.0)
(1.0, 1.0)
(1.0, 0.0, 0.0, 1.0)

We get the numpy array for the image and visualize it:

In [6]:
im_np0 = sitk.GetArrayFromImage(im0)
In [7]:
plt.imshow(im_np0, cm.gray)
Out[7]:
<matplotlib.image.AxesImage at 0x11cdb3a90>

Let's do the same for the second image:

In [8]:
input_image0 = os.path.join(TubeTK_BINARY_DIR, 'MIDAS_Data/ES0015_Large_Wo_offset.mha')
im1 = sitk.ReadImage(input_image0)
print im1.GetOrigin()
print im1.GetSpacing()
print im1.GetDirection()
(0.0, 0.0)
(1.0, 1.0)
(1.0, 0.0, 0.0, 1.0)

In [9]:
im_np1 = sitk.GetArrayFromImage(im1)
In [10]:
plt.imshow(im_np1, cm.gray)
Out[10]:
<matplotlib.image.AxesImage at 0x11cfb6f90>

Let's check if the spacing and direction are compatible:

In [11]:
im0.GetSpacing() == im1.GetSpacing() and im0.GetDirection() == im1.GetDirection()
Out[11]:
True

We see that im0 and im1 are in fact compatible, but the origin of im0 is at (200, 200).

Merging - Example 1

In this example, we just want to merge our two images (without registration). Let's build the command-line arguments (The output image will be written to /tmp/merged.mha).

In [12]:
output_image = os.path.join(TubeTK_BINARY_DIR, 'Temporary/Python.MergeAdjacentImages-Ex1.mha')

cmd = [os.path.join(TubeTK_BINARY_DIR, 'bin/MergeAdjacentImages'),
       '-i 0', # Number of iterations ... here i=0, which means no registration,
       input_image0, # First image to merge
       input_image1, # Second image to merge
       output_image
      ]

Let's execute that command (via the subprocess module):

In [13]:
import subprocess
subprocess.call(cmd)
Out[13]:
0

... and check if the output image /tmp/merged.mha was actually written to disk:

In [14]:
print os.path.exists(output_image)
True

We are now ready to visualize the result:

In [15]:
out_im = sitk.ReadImage(output_image)
print out_im.GetOrigin()
print out_im.GetSpacing()
print out_im.GetSize()
(0.0, 0.0)
(1.0, 1.0)
(712, 712)

In [16]:
plt.imshow(sitk.GetArrayFromImage(out_im), cm.gray)
Out[16]:
<matplotlib.image.AxesImage at 0x11cfe6a50>

We see that the output image is larger by 212 pixel in both dimensions, since the second image's origin was at (200, 200) and the image size of both images was 512 times 512 pixel.

Merging - Example 2

We can also add some padding (e.g., 50 pixel on each side). For that we modify cmd as follows:

In [17]:
output_image = os.path.join(TubeTK_BINARY_DIR, 'Temporary/Python.MergeAdjacentImages-Ex2.mha')

cmd = [os.path.join(TubeTK_BINARY_DIR, 'bin/MergeAdjacentImages'),
       '-i 0', # Number of iterations ... here i=0, which means no registration,
       '-b 50,50', # This adds a white border around the second image (50 pixel each side)
       input_image0,
       input_image1,
       output_image
      ]
In [18]:
subprocess.call(cmd)
Out[18]:
0
In [19]:
plt.imshow(sitk.GetArrayFromImage(sitk.ReadImage(output_image)), cm.gray)
Out[19]:
<matplotlib.image.AxesImage at 0x11e5ac710>

Merging - Example 3

Let's do the same example WITH rigid registration.

In [26]:
output_image = os.path.join(TubeTK_BINARY_DIR, 'Temporary/Python.MergeAdjacentImages-Ex3.mha')

cmd = [os.path.join(TubeTK_BINARY_DIR, 'bin/MergeAdjacentImages'),
       input_image1,
       input_image0,
       output_image
      ]
In [27]:
subprocess.call(cmd)
Out[27]:
0
In [28]:
plt.imshow(sitk.GetArrayFromImage(sitk.ReadImage(output_image)), cm.gray)
Out[28]:
<matplotlib.image.AxesImage at 0x124d42a10>
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