first of all: this is a cool tool, kudos for making it publicly available!
My issue: I am trying to use pims.open to access a sequence of image files stored as compressed nifti files (.nii.gz). When this did not work (UnknownFormatError: Could not autodetect how to load a file of type gz. Try manually specifying a loader class, e.g. Video(/home/user/Desktop/testfile.nii.gz), I tried it on uncompressed nifti files (.nii), but the same error occured.
The bit ...how to load a file of type gz indicates that the "double-dot extension" .nii.gz is not correctly parsed.
Based on the documentation, reading niftis should be possible, since PIMS has access to the imageio reader functionality, which in turn can call an ITK plugin to read .nii as well as .nii.gz (according to the docs).
Am I missing something? Is there a way to tell PIMS where to look for the reader function?
If you could point me towards the relevant sections in the codebase, I would try and implement a solution in a dedicated PR.
Hello dear PIMS people,
first of all: this is a cool tool, kudos for making it publicly available!
My issue: I am trying to use pims.open to access a sequence of image files stored as compressed nifti files (.nii.gz). When this did not work (
UnknownFormatError: Could not autodetect how to load a file of type gz. Try manually specifying a loader class, e.g. Video(/home/user/Desktop/testfile.nii.gz), I tried it on uncompressed nifti files (.nii), but the same error occured.The bit ...
how to load a file of type gzindicates that the "double-dot extension" .nii.gz is not correctly parsed.Based on the documentation, reading niftis should be possible, since PIMS has access to the imageio reader functionality, which in turn can call an ITK plugin to read .nii as well as .nii.gz (according to the docs).
Am I missing something? Is there a way to tell PIMS where to look for the reader function?
If you could point me towards the relevant sections in the codebase, I would try and implement a solution in a dedicated PR.
Thank you in advance!