Asldro

Fixed
- Bug that caused an error if the SNR was set to 0.

Changed
- Default 'image_type' attribute of image containers is now 'REAL_IMAGE_TYPE'
- PhaseMagnitudeFilter now accepts additional 'image_type'
- Supplied ground truths (hrgt_icbm_2009a_nls_3t and hrgt_icbm_2009a_nls_31.5t)
have had their transit times changed to 0.8s for Grey Matter and 1.2s for
White Matter.

Added
- Allow using an input (external) HRGT file.
- Modulation of ground truth quantities by a scale and offset value

Fixed
- Bug that caused ground truth not to be resampled before being output

Changed
- JSON loader filter can take any JSON schema (or none)

Added
- Inversion recovery MRI model
- Image container metadata
- Acquire MRI Image Filter (combines MRI Signal, transform/resampling, noise)
- Append metadata filter
- Combine time-series images filter
- Phase-magnitude filter
- CLI tool to output the HRGT files
- BIDS output
- Output of structural and ground truth data
- 1.5T and 3T HRGT files
- Allow overriding the ground truth values in the input parameter file

Changed
- New input parameter file format (allows multi-series output)
- GE MRI signal model now allows arbitrary flip-angle

Added
- Project repository set up with Continuous integration,
Continuous testing (pytest, tox), Repository structure,
Versioning information, Setup configuration,
Deployment configuration
- Autoformatting and linting rules set up
- Pipe-and-filter architecture
- Ground truth data based on the ICBM 2009a Nonlinear Symmetric brain atlas
- NiftiImageContainer and NumpyImageContainer
- Ground truth JSON validation schema
- Filters for fft and ifft
- Complex noise filter
- Filter blocks (chains of filters)
- Parameter validation module
- GKM filter (PASL, CASL, pCASL)
- MRI signal filter
- Sphinx documentation generation (and documentation)
- Command line interface
- Affine matrix transformation filter (output sampling)
- README generator
- PyPI deployment
- CLI tool to output example model parameter file