Image writer with itk backend to support more output image formats

[wyli]

Is your feature request related to a problem? Please describe.
The SaveImage transform should be extended to support writing output in different formats using ITK.

MONAI/monai/transforms/io/array.py

Lines 260 to 261 in 830f8bb

	if output_ext in (".nii.gz", ".nii"):
	self.saver = NiftiSaver(

the current nifti output doesn't work well with Slicer Project-MONAI/MONAILabel#211

see also InsightSoftwareConsortium/ITK#2663

[Nic-Ma]

Hi @wyli ,

I have a question about the feature request of this ticket:
Currently, we have nifti_saver & nifti_writer and png_saver & png_writer and SaveImage transform, maybe there are 2 options:

1. If we just want to add support to save in DICOM format, we can add dicom_saver & dicom_writer based on ITK APIs.
2. If want to support many other formats, I think we need to totally refactor the saving part and make it just like the inverse of the ImageReaders and LoadImage:
   (1). Remove nifti_saver & nifti_writer and png_saver & png_writer.
   (2). Add NibabelWriter for NIfTI, PILWriter for PNG, JPG, JPEG, BMP, ITKWriter for any other formats.
   (3). Use SaveImage transform as high-level API, mapping to LoadImage.

What do you think or you guys have other ideas?

Thanks.

[wyli]

I think as an initial step we could add a minimal itk_writer and make it an option in SaveImage in v0.7. The goal is to encourage the use of SaveImage and we'll refactor the underlying implementation later (beyond 0.7) -- For refactoring the writer, option 2 looks good, we still need to review the quality of these writer APIs and probably get comments/proposals from the working groups.

[Nic-Ma]

Hi @wyli ,

Plan makes sense, we can develop a itk_writer and call it in SaveImage directly instead of a itk_saver layer. When it's done in v0.7, we can refactor nifti_writer & nifti_saver to nibabel_writer, and refactor png_writer & png_saver to pil_writer based on the same pattern of itk_writer.
I can develop a PR for ITKWriter with the similar design of ITKReader, may not support many formats in the first step.

Thanks.