Adds --ref_dicom option to nii2dcm

[tomaroberts]

Resolves #14

Allows user to specify reference DICOM from which DICOM attributes are transferred to nii2dcm DICOM

Usage example: nii2dcm input/SVR-output.nii.gz output --ref_dicom ref_dicom_example/ref_dicom.dcm --dicom_type SVR

Some notes:

• Attributes transferred from reference DICOM override any initialised previously
• So far designed using a 3D Siemens MRI DICOM as reference (and informed by previous work with Philips 3D MRI DICOMs)
• DICOMs open in ITK-Snap and Horos
• I have been selective with which Attributes are transferred. There may be errors, I may have been too permissible (Tags not to transfer because they are more likely to cause import failures) or there are omissions (Tags not transferred because I missed them).
• I have copied over large SQ Sequence blocks – suspicious these might fall into the too permissible category and cause more issues than they are worth.

TODO:

• [x] Test import on Siemens MRI scanner
• [x] Extract the attributes_to_transfer list from dcm_writer.py and put in the DicomMRI and DicomMRISVR subclasses. This makes more sense because then different types of DICOM can have their own unique Attributes to transfer.
• [ ] Decide how best to deal with Times, e.g.: StudyTime/StudyDate can be transferred, but do I transfer SeriesTime or create myself to avoid conflict with acquired SeriesTimes? Latter feels 'truer'.
• [ ] Implement logger
• [x] Convert modules to classes

[tomaroberts]

11/08 – tested on Siemens scanner using --ref_dicom option with Siemens 3D dataset – nii2dcm derived dataset appeared on scanner in correct Study! 🥳 🥳 🥳

15/08 – created modules folder containing Module subclasses. Better for creating Composite IODs