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Support 3D Images Natively #49

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robtoth opened this issue Jul 1, 2020 · 0 comments
Closed

Support 3D Images Natively #49

robtoth opened this issue Jul 1, 2020 · 0 comments
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@robtoth
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enhancement New feature or request internal Tasks meant for internal development by project maintainers.
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Initial Presentat...

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robtoth commented Jul 1, 2020

Instead of looping through the third dimension as slices, create the co-occurence matrix from the surrounding 3D voxels.

This will requires greycomatrix to be configured to process 3D images prior to passing the resulting matrix to the mahotas library for haralick calculations.

If the grey levels are 64, then the co-occurence matrix will still be 64x64, but will have pulled its data from surrounding voxels, not just surrounding pixels from the current slice.
@robtoth robtoth added the enhancement New feature or request label Jul 1, 2020
@robtoth robtoth mentioned this issue Jul 30, 2020
Closed
robtoth added a commit to Theta-Tech-AI/collageradiomics that referenced this issue Jul 31, 2020
@robtoth
Added a variable and error checking to support 3D numpy arrays. Issue r…
6488df7 
…adxtools#49
robtoth added a commit to Theta-Tech-AI/collageradiomics that referenced this issue Jul 31, 2020
@robtoth
In the case of 2D, the image and mask are reshaped to a 3D numpy arra…
01f2649 
…y with a depth of 1. Issue radxtools#49
robtoth added a commit to Theta-Tech-AI/collageradiomics that referenced this issue Jul 31, 2020
@robtoth
Made cropping of the image based on a 3D numpy array. Issue radxtools#49
868ca5b
robtoth added a commit to Theta-Tech-AI/collageradiomics that referenced this issue Jul 31, 2020
@robtoth
Pass in the dx,dy,dz to the svd calculation instead of just dx,dy. Is…
18abdea 
…sue radxtools#49
robtoth added a commit to Theta-Tech-AI/collageradiomics that referenced this issue Jul 31, 2020
@robtoth
Moved the code to calculate the dominant angle image to its own funct…
ab45d00 
…ion. Issue radxtools#49
robtoth added a commit to Theta-Tech-AI/collageradiomics that referenced this issue Jul 31, 2020
@robtoth
Moved the calculation of the haralick features to its own function, a…
66fe9c8 
…nd initialize the output with NaNs. It also loops through slices in the case of 3D. Issue radxtools#49
robtoth added a commit to Theta-Tech-AI/collageradiomics that referenced this issue Jul 31, 2020
@robtoth
Calculate secondary angle for 3D collage. Issue radxtools#49
202035a
@robtoth robtoth added the internal Tasks meant for internal development by project maintainers. label Jul 31, 2020
robtoth added a commit to Theta-Tech-AI/collageradiomics that referenced this issue Jul 31, 2020
@robtoth
Used the itertools product instead of 3 nested for loops for the 3 di…
1a5dd74 
…mensions of dominant angle calculations. Closes radxtools#49
robtoth added a commit to Theta-Tech-AI/collageradiomics that referenced this issue Jul 31, 2020
@robtoth
Made the jupyter notebook use the new 3D functionality. Issue radxtoo…
03cf177 
…ls#49
nathanhillyer pushed a commit to Theta-Tech-AI/collageradiomics that referenced this issue Aug 3, 2020
@robtoth @nathanhillyer
Added a variable and error checking to support 3D numpy arrays. Issue r…
26a4619 
…adxtools#49
nathanhillyer pushed a commit to Theta-Tech-AI/collageradiomics that referenced this issue Aug 3, 2020
@robtoth @nathanhillyer
In the case of 2D, the image and mask are reshaped to a 3D numpy arra…
adfa239 
…y with a depth of 1. Issue radxtools#49
nathanhillyer pushed a commit to Theta-Tech-AI/collageradiomics that referenced this issue Aug 3, 2020
@robtoth @nathanhillyer
Made cropping of the image based on a 3D numpy array. Issue radxtools#49
0f82a19
nathanhillyer pushed a commit to Theta-Tech-AI/collageradiomics that referenced this issue Aug 3, 2020
@robtoth @nathanhillyer
Pass in the dx,dy,dz to the svd calculation instead of just dx,dy. Is…
b63c809 
…sue radxtools#49
nathanhillyer pushed a commit to Theta-Tech-AI/collageradiomics that referenced this issue Aug 3, 2020
@robtoth @nathanhillyer
Moved the code to calculate the dominant angle image to its own funct…
11eec6d 
…ion. Issue radxtools#49
nathanhillyer pushed a commit to Theta-Tech-AI/collageradiomics that referenced this issue Aug 3, 2020
@robtoth @nathanhillyer
Moved the calculation of the haralick features to its own function, a…
dd52332 
…nd initialize the output with NaNs. It also loops through slices in the case of 3D. Issue radxtools#49
nathanhillyer pushed a commit to Theta-Tech-AI/collageradiomics that referenced this issue Aug 3, 2020
@robtoth @nathanhillyer
Calculate secondary angle for 3D collage. Issue radxtools#49
92acab9
nathanhillyer pushed a commit to Theta-Tech-AI/collageradiomics that referenced this issue Aug 3, 2020
@robtoth @nathanhillyer
Made the jupyter notebook use the new 3D functionality. Issue radxtoo…
f1a48ca 
…ls#49
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