nifti saver squeeze dims

[rijobro]

Fixes #1678.

Description

Currently NiftiSaver (therefore default SaveImage and SaveImaged) saves images as (H,W,D,C), even if input image had no channel dimension, or was only a 2D image.

This PR allows users to squeeze trailing singleton dimensions. If C==1, image will be saved as (H,W,D). If D is also == 1, image will be saved as (H,W). If D==1, but C>1, image will still be saved as (H,W,D,C) (to avoid channel dimension being interpreted as depth).

I also changed the saved path from /some/path/filename/filename.nii.gz to /some/path/filename.nii.gz, as I assumed the former was a mistake. I can undo this if it was intentional. EDIT: I reverted this for backwards compatibility, but I still find it ugly.

Status

Ready

Types of changes

• Non-breaking change (fix or new feature that would not break existing functionality).
• New tests added to cover the changes.
• Integration tests passed locally by running ./runtests.sh --codeformat --coverage.
• Quick tests passed locally by running ./runtests.sh --quick.
• In-line docstrings updated.
• Documentation updated, tested make html command in the docs/ folder.

[rijobro]

fixes #1677.

[wyli]

thanks! looks good to me. (there's a similar workaround in niftynet https://github.com/NifTK/NiftyNet/blob/935bf4334cd00fa9f9d50f6a95ddcbfdde4031e0/niftynet/io/misc_io.py#L441-L450 proposed by @hjmjohnson )

[wyli]

for the file path, I think it's originally from Clara Train where we want to save some other relevant predictions along with each .nii.gz file, /some/path/filename is a default folder to collect those predictions