Geodesic dilation inside 3D Binary Mask
eric.mo...@gmail.com
I have been searching online for 3D Mathematical Morphology tools, in particular geodesic dilation, and I have found your wonderful Python package, Mamba. I would like to know if Mamba could be used for my research. By the way, I am studying in Paris, so if my problem seems complicated, I would very much be willing to come to your lab in person.
In the photo I attached, I would like to apply a 3D geodesic dilation of the red dot (where the crosshairs are) inside the blue mask. The attached image is a brain imaging file (.nii). I can load both of these volumes in python (blue mask and red dot) and convert them to a numpy array (size 100x120x58). They are both binary masks (black = 0, blue = 1, red = 1). What I would like to do then is use the tools in Mamba to apply a geodesic dilation on the red binary volume constrained by the blue binary volume. Is this possible?
Best regards,
Eric Moulton
P.S. I am also having some trouble downloading Mamba and Mamba3D on my computer. When I try to import Mamba3D in Python, I get the following error message:
In [4]: import mamba3D
Missing PIL or PILLOW libraries - See MAMBA User Manual
Missing Mamba library - http://www.mamba-image.org
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-4-01c17093f2e0> in <module>()
----> 1 import mamba3D
/usr/local/lib/python2.7/dist-packages/mamba3D/__init__.py in <module>()
6 # Mamba imports
7 try:
----> 8 import mamba
9 _mb_version = mamba.VERSION.split('.')
10 if int(_mb_version[0])!=1 and int(_mb_version[1])!=1:
/usr/local/lib/python2.7/dist-packages/mambaIm/mamba.py in <module>()
10 import mambaCore
11 import mambaUtils as mbUtls
---> 12 from mambaDisplay import getDisplayer, setMaxDisplay, setMinDisplay
13 from mambaError import raiseExceptionOnError, raiseWarning, MambaError
14
/usr/local/lib/python2.7/dist-packages/mambaIm/mambaDisplay.py in <module>()
18 except ImportError:
19 try:
---> 20 from PIL import ImageTk
21 from PIL import Image
22 except ImportError:
ImportError: cannot import name ImageTk
---
I have tried redownloading the PIL library, but the only package inside of it that is missing is ImageTk! I have followed the instructions in the readme of the Mamba.1.1.3.zip file downloaded from the website, and the instructions of the Mamba3D users guide.
eric.mo...@gmail.com
I am able to import mamba3D in python now. The main problem now is to use a geodesic dilation on my 3D array.
Thank you,
Eric
eric.mo...@gmail.com
I guess I had a stroke of inspriation after being stuck, and I figured out what to do, so I will share my code for those who would like to do something similar. Just for a note, my .nii.gz images are of size 100x120x58, but I had to extend the second dimension to 128 (which is why I append 8 zero matrices onto my image arrays, but then I remove it at the end).
I've also shared the result of the geodesically eroded point in the image below (radius = 1 (red), 2 (blue), 3 (green), 4 (yellow) )
If I were to use these results in a publication, how would you prefer that I cite you? Thanks a lot for such a great Python package !
