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vol.load_dicom() implementation #30
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Commits on Mar 26, 2021
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The parenthesis in the macro UPDATE and INTERPOLATE are causing problems when compiling on windows. See arcadelab#26 for more details.
Maximilian Rohleder authored and Maximilian Rohleder committedMar 26, 2021 Configuration menu - View commit details
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Commits on Mar 30, 2021
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Started implementing from scratch
The computation of lps_from_ijk turned out to be harder than anticipated. Reason for that is the immensely complex and horribly covered dicom standard. Trying to use nibabel next to outsource all the error handling to another lib.
Maximilian Rohleder authored and Maximilian Rohleder committedMar 30, 2021 Configuration menu - View commit details
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Using nibabel.nicom.dicomwrappers.MultiframeWrapper to construct the affine transform from the available dicom tags. Evidently this is complex enough to _not_ maintain it in this project. See this post to get a feeling for the complexity: https://nipy.org/nibabel/dicom/dicom_orientation.html#defining-the-dicom-orientation. The used class warns, that the exposed functionality is not well tested. I will verify that it works with our datasets.
Maximilian Rohleder authored and Maximilian Rohleder committedMar 30, 2021 Configuration menu - View commit details
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Commits on Mar 31, 2021
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Using nibabel.nicom.dicomwrappers.MultiframeWrapper seems not as well fitting as expected. The class was conceptualized for phillips dicoms and there seems to be a non-trivial difference. Decided to implement the affine transform computatio from scratch following these resources: https://nipy.org/nibabel/dicom/dicom_orientation.html#defining-the-dicom-orientation https://mrohleder.medium.com/coordinate-systems-in-medical-data-science-a-rant-90394f60b27 https://github.com/nipy/nibabel/blob/master/nibabel/nicom/dicomwrappers.py
Maximilian Rohleder authored and Maximilian Rohleder committedMar 31, 2021 Configuration menu - View commit details
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Add description and remove parameter
Same number of parameters as from_nifti() now.
Maximilian Rohleder authored and Maximilian Rohleder committedMar 31, 2021 Configuration menu - View commit details
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Commits on Apr 3, 2021
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The difference in indexing between dicom and this framework were previously dealt with in the affine matrix by switching the columns of i and j. Now, we change the internal layout of the supplied volume prior after loading and leave the affine transform untouched.
Maximilian Rohleder authored and Maximilian Rohleder committedApr 3, 2021 Configuration menu - View commit details
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Removed unnecessary import and minor refactoring
Grouped the dicom tags by per-frame and per-slice attributes for better readability. Removed not needed InvalidDicomError import.
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Remove CUDA commit from this pull-request
The parentheses in the CUDA kernel are a different topic and should be dealt with in a seperate thread. Removing that commit from the history of this branch. This reverts commit 8f45483.
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