Dear ITK devs,
Many thanks for creating such a solid tool. I am currently trying to migrate from SimpleITK to ITK python because of LabelGeometryImageFilter’s ability to calculate orientation as well. I would like to calculate the orientation of the binary label objects for my morphometric analysis.
I installed ITK 5.2.1.post1 using PIP (itk-filtering included, OS: Linux and Mac) . However, when I try to use LabelGeometryImageFilter using “itk. LabelGeometryImageFilter” - I get the following error: AttributeError: module ‘itk’ has no attribute ‘LabelGeometryImageFilter’. Am I doing something wrong? Any guidance would be highly appreciated.
Many thanks,
Lalith
Hello @LalithShiyam
Possibly take a look at SimpleITK’s LabelShapeStatisticsImageFilter, it computes orientation information too. For a detailed usage example, characterizing the shapes of bacteria, see this jupyter notebook.
LabelGeometryImageFilter
is part of Review
module, and is not built by default. To get it, you should compile ITK with Python wrapping and Module_ITKReview
turned on.
Many thanks will do so!
Many thanks - will check it out again
There are some issue with some computations in the LabelGeometryImageFilter not correctly taking into account the image’s direction cosine matrix and/or the pixel spacing. These have been corrected in the implementation in the ITK LabelMap framework. Please look at the LabelImageToShapeLabelMapFilter for an updated implementation.