pixel_array orientation

[tionichm]

I was wondering whether pydicom.dataset.Dataset.pixel_array always returns the CT image in a particular orientation. Is it guaranteed to be left ascending and poserior ascending?

I think that my confusion stems from trying to put together what I've read on "Load CT slices and plot axial, sagittal and coronal images" tutorial, the documentation on pydicom.dataset.Dataset.pixel_array, and my recent reading into the C.7.6.2.1.1 Image Position and Image Orientation and C.7.3.1.1.2 Patient Position sections of the DICOM format.

What I want to achieve is to have the images from my CT scans in a standard LPS orientation - do I need to do this myself, or does pydicom take care of this? The z-axis is a non-issue, because I can use the Patient Position to determine the direction of the series, as discussed in this thread.

[darcymason]

Pydicom is really just a container for the raw DICOM data, it does not orient or scale the pixel data in any way other than to shape the numpy array when accessed through pixel_array. The interpretation is up to user code via ImageOrientationPatient and other data elements as you have mentioned.

[tionichm]

Cool - this was exactly what I needed to know. You've been a great help.