# spant 4.4.0
* Fix for Philips svs spar/sdat voxel geometry.
* Bug fixes for match_lineshape function.
* Added zero_spec_threshold function.
* Added set_spec_values function.

# spant 4.3.0
* Bug fix for mr_data2bids function.
* Bug fix for testing for GE data in fit_svs.
* Added fit_svs_btrg_v1 function as a simple wrapper for fit_svs with defaults
adjusted to improve the analysis of lower quality brain tumour spectra.

# spant 4.2.0
* Added rm_basis_elements function.
* Added plot_tqn_fit_csv function.
* Test fix for NIfTI MRS reader.

# spant 4.1.0
* Update to lsei.f to fix a warning produced by GCC 16.
* Changed the default segmentation method to rpyants for fit_svs.

# spant 4.0.0
* qr.solve reverts to ginv for rats in rare cases where qr.solve fails.
* fit_svs updated to only accept a single argument for remove_basis.
* Bug fix for Siemens DICOM reader.
* Added support for T1 tissue segmentation using binary installation of ANTs : 
https://github.com/antsx/ants
* Added support for T1 defacing with the FaceOff method : 
https://github.com/srikash/FaceOff
* Added cross-platform support for T1 tissue segmentation using ANTs via the
rpyANTs package : https://github.com/dipterix/rpyANTs

# spant 3.9.0
* Added extra pre_align options to fit_svs.
* Added extra plot to fit_svs html output to help diagnose frequency alignment
problems.

# spant 3.8.0
* Added deface option to fit_svs.
* Added overwrite option to fit_svs.
* fit_svs and fit_svs_edited now accept vectorised file inputs for batch
analyses.

# spant 3.7.0
* Added lb_renoise function for fMRS analyses.
* Added paths2df function to help extract ID fields from a vector of paths.
* Added trim_paths and match_files functions to help with filesystem based data 
discovery.

# spant 3.6.0
* Added mean_dyns_scheme function.
* Millisecond option added to plot x scale.
* Added read_basis_niidir and write_basis_niidir functions for import/export
of basis sets stored as a group of NIfTI MRS files.

# spant 3.5.0
* Added a function to help bids sorting of MRS and MRI data : mr_data2bids.
* Extra options to fit_svs : dfp_corr_ref_subset and w_ref_subset.
* fit_svs default now uses the mean of all available water reference scans,
rather than just the first dynamic. Set w_ref_subset = 1 to reproduce previous
results.

# spant 3.4.0
* Added a function to read DKD's sLASER MoCo log file.
* Bug fix for TE parameter determination from Siemens IMA files.

# spant 3.3.0
* Added voxel render on MRI images to fit_svs.
* Added voxel segmentation render and support to fit_svs.
* Bug fix for TE parameter determination from Siemens TWIX files.
* Added extra output data from fit_svs to aid group analyses.

# spant 3.2.0
* Individual metabolite plots in the html report are now labelled to workaround
an R Markdown bug where identical plots (eg when signal is zero) are sometimes
not shown.
* Added get_hrf function to spant namespace.
* Tentative support for a command line interface : spant_fit_svs.
* Tentative support for LCModel analysis in the fit_svs function and cli.

# spant 3.1.0
* Tentative implementation of a standard single voxel MRS processing pipeline
function: fit_svs.
* spant user guide has been added to the project: 
https://spantdoc.wilsonlab.co.uk/
* Implemented basis caching for sim_basis.
* scale_amp_molar function has been depreciated. Please use scale_amp_legacy
for LCModel style concentration scaling instead.
* Assumed T1 and T2 relaxation values for molal concentration scaling have been
updated. See the user guide for details.

# spant 2.24.0
* Added argument to adjust the legend font size in ortho3 function.
* Improved metabolite simulation performance thanks to the expm package recently
adding support for complex matrices.

# spant 2.23.0
* abfit options for lipid and MM maximum broadening and maximum frequency shift
now default to be the same as the metabolite values unless explicitly changed.
* Added function to calculate the correlation matrix from a basis_set.
* Fix for RDA files where a comma is sometimes used as a decimal point.

# spant 2.22.0
* Added find_bids_mrs and mrs_data2bids helper functions.
* Improved handling of CMRR semi-LASER SVS water reference scans.
* Added functions for GLS coil combination.

# spant 2.21.0
* Fixed compiler warnings for Fortran code.
* Added glm_spec function.
* Added add_noise_spec_snr function.

# spant 2.20.0
* Added vertical line colour and linetype options for stackplots.
* Added option to give Y axis labels in units of seconds for spectrograms.

# spant 2.19.0
* Removed dependency on smoother package.
* Added functions for generating BOLD and trapezoidal response shapes.

# spant 2.18.0
* Improved automated file type detection.
* Bug fixes for DICOM MRS reader.
* scale_spec function now works with basis set objects.
* Added invert_fit option to plotting methods.

# spant 2.17.0
* Simulation duration output is now rounded to 2dp.
* sim_basis now accepts a character vector of molecular names.
* Added get_1h_brain_basis_names function.

# spant 2.16.0
* Added subset option to mean_dyns function.
* Added vline option to plot.
* Added common 31P brain metabolites.
* Added verbose option to sim_basis.

# spant 2.15.0
* An SNR estimate of zero in comb_coils is now a failure case.
* Bug fix for GE pfile reader header revision 20.
* Added a function for finding valid MRS files : find_mrs_files.

# spant 2.14.0
* Added vline argument to stackplot function.
* Added functions to set MRS data TR and number of transients.

# spant 2.13.0
* Improved defaults for sim_brain_1h function.
* Added scale_basis_amp function.
* Added crop_basis function.

# spant 2.12.0
* Amplitude scaling functions duplicate water reference amplitudes when
sensible.
* Added hline option to the mrs_data plot function.

# spant 2.11.0
* Bug fix for Siemens RDA slice thickness detection.
* ProtocolName is now read from GE p-files.

# spant 2.10.0
* Tentative support for UIH DICOM MRS format.
* Improved support for reading GE p-files.
* Added a WIP function to export a one-page summary pdf of the fit result
"one_page_pdf".

# spant 2.9.0
* Bug fix when using align function with masked data.
* mean_dyn_blocks returns the input data when block_size is set to 1.

# spant 2.7.0
* Added Manufacturer tag to metadata.
* Added mask_xy_corners and mask_xy_ellipse functions.
* Added functions to fit T1 and T2 relaxation curves.
* Updated CI checks.

# spant 2.6.0
* Masked spectra plotted with image are now shown with a value of zero.
* Added function to read .pta files - read_pulse_pta.
* Added a function to make basis set objects from a directory of LCModel
formatted RAW files - make_basis_from_raw.
* Added horizontal line to fit result plots.
* Improvements to reading LCM .raw files with variable numerical columns.

# spant 2.5.0
* Improved function documentation for water concentration scaling.
* Added water and tCr scaling examples to the introduction vignette.
* Better error checking for reading ima files.
* read_basis function improved to work with variable formatting.
* Improved default method of time-domain signal amplitude estimation.
* Added helper functions for working with basis set objects: 
scale_basis_from_singlet, resample_basis and get_basis_subset.
* Bug fix for STEAM basis simulation being incorrectly scaled for internal
water scaling methods.

# spant 2.4.0
* Performance improvement for reading VD format TWIX files.
* Function added to scale all metabolite levels by a set value
(scale_amp_ratio_value).

# spant 2.3.0
* Verbose option added to read_ima_coil_dir and read_ima_dyn_dir functions.
* Support added for reading jMRUI txt formatted MRS data.
* sim_brain_1h default sequence changed to semi-LASER and line-broadening option
added.
* Bug fix for reading LCModel RAW files.
* Bug fix for HSVD filter when only 0 or 1 components are found in the filter
region.
* Improved removal of unwanted data points for reading TWIX formatted data.
* A json sidecar is automatically written when exporting NIfTI MRS formatted
data.
* TWIX reader improved to only read data points from the last scan in the file.
This also fixes a rare bug.

# spant 2.2.0
* peak_info function now works with masked datasets.
* Bug fix for HSVD function not working with frequency domain data.
* Bug fix for TWIX affine calculation when not using power of two matrix
dimensions.
* New function (crop_td_pts_pot) to round a dataset length down to the nearest
power of 2.
* Added ret_metab_only option to comb_coils.
* rats now only returns the corrected data by default, note this could break old
code.

# spant 2.1.0
* y-axis label can now be changed with a new argument (yaxis_lab) to
plot.mrs_data.
* Segmentation files are now checked for non-integer values.
* gridplot has better row and col number defaults for MRSI, and has a bug fix
for plotting masked spectra.
* Updated functions for dealing with lists of MRSI datasets.
* Bug fix for crop_xy function when working with odd matrix sizes.

# spant 2.0.0
* magrittr pipe (%>%) is no longer loaded together with spant now the base pipe
is part of R. Vignettes and tests have been updated to use the base pipe.
* NIfTI MRS writer no longer fails when dealing with a NULL affine matrix.
* Bug fix for NIfTI MRS writer, where frequency domain data was not correctly
converted to time-domain before export.

# spant 1.22.0
* Added MSM and acetone to the set of internally defined molecules.
* write_mrs_nifti function removed from userspace. write_mrs should be used
instead.
* set_td_pts and crop_td_pts now work with lists of spectra.
* Multiple files can now be written by passing a list of spectra to write_mrs.

# spant 1.21.0
* Bug fix for get_mrsi_voi function due to incorrect rounding of MRSI matrix
dimensions in some cases.
* Added mask_fit_res function.
* Option added to get_2d_psf function to ensure odd output dimensions.
* Bug fix for using rats on datasets with masked voxels.
* Added spec_decomp function.
* Added ret_scale_factor option to scale_spec function.

# spant 1.20.0
* Options added to ft_dyns to return the modulus of the 2D spectra and to
pre-transform the chemical shift axis if needed.
* Bug fix for printing lists of mrs_data objects.
* comb_coils function now supports lists of mrs_data objects.
* IMA reader now respects the verbose option in read_mrs.
* Bug fix for get_mrsi_voi ignoring the ker argument.
* Bug fix for reading Siemens TWIX files.

# spant 1.19.0
* Added sum_mrs_list function.
* Bug fix for operating on mrs_data with single values that aren't numeric
types. For example, multiplying mrs_data by a single complex number now works.
* A number of common preprocessing functions now operate on lists of mrs_data
objects.
* Change to NIfTI MRS reader to fix a failing test when using the development
version of RNifti.

# spant 1.18.0
* Better behaviour when using stackplot with single spectra datasets.
* Better behaviour when using image with single spectra datasets.
* Bug fix for reading MEGA-PRESS data in TWIX format.
* Better error checking for lists of spectra.
* Bug fix for calculating NAA linewidth from MEGA-PRESS data.

# spant 1.17.0
* New function added (recon_twix_2d) for reconstructing basic phase encoded twix
2D MRSI data.
* File name argument for read_mrs now permits globbing, eg read_mrs("*.dcm").
* Improved plotting of metabolite maps containing infinite values.
* Improvements to GE p-file reader.
* Bug fix for TWIX MRSI voxel dimensions.
* get_mrsi2d_seg now returns partial volume maps as well as a data frame.
* Improved error handling for spec_op function.
* apodise_xy can now be applied to multi-coil and dynamic datasets.

# spant 1.16.0
* The package has been published in the Journal for Open Source Software :
"spant: An R package for magnetic resonance spectroscopy analysis. JOSS 2021,
6(67), 3646".
* The basis result of the HSVD function is now an mrs_data object.
* The complete model signal is now output by the HSVD function.
* image function x-axis updated to be consistent with other plotting methods.
* Minor refactor of the simulation code and a dependency swap from complexplus
to exmp packages.

# spant 1.15.0
* Added a unit test for reading and writing LCM .basis formatted files.
* Added FWHM estimates for tCr and tCho in ABfit.
* Added water suppression efficiency and water FWHM measures to the diagnostic
output of svs_1h_brain_analysis.
* Added get_head_dyns and get_tail_dyns to return the first and last dynamic
scans within a dataset.
* Fixed CI errors.
* Improved installation instructions.
* Removed comb_csv_results function and reduced the number of required packages.

# spant 1.14.0
* Added glycerol simulation parameters, e.g. get_mol_paras("glyc").
* Bug fix for read_ima_* functions.
* Improved y = 0 baseline for stackplot when setting bl_lty parameter.
* Removed norm_mrs function and replaced with scale_spec for simple data
scaling tasks, eg scaling based on the integration of a spectral region.
* Added spec_op function for performing simple summary operations on spectral
segments.
* Changed the name of scale_mrs function to scale_mrs_amp.
* Added mean_mrs_list function.
* Improved LCM RAW and BASIS readers (contribution from Alex Craven).

# spant 1.13.0
* ABfit frequency shifts limits are now specified in ppm rather than Hz to
improve consistency between field strengths.
* NAA linewidth is now estimated and output by ABfit when NAAG is absent - 
useful for BRAINO phantom scans.
* Warning now given when spectra are mathematically combined and are not both
in the same time/frequency domain.
* sum_mrs function added to simplify combining spectra within a pipe.
* scale_mrs function added to simplify scaling a spectrum within a pipe.
* add_noise function added to simplify generating simulated data with a pipe.
* hsvd_filt function now accepts a frequency range in ppm units and gives the
option to return the model rather than the filtered data.
* Bug fix for hsvd_filt function where the max_damp argument was ignored.
* SVS reference scans, found in some TWIX files, are now removed by default.
* Bug fix for reading list/data when only one coil element is used.

# spant 1.12.0
* Added 2HG and citrate simulation parameters. e.g. get_mol_paras("2hg").
* Better print output for molecular definitions.
* Added metabolite and basis simulation vignettes.
* Bug fix for setting the ppm reference when reading LCModel RAW files.
* Bug fix for ABfit CRLB calculation of combined signals, eg tNAA, tCr.

# spant 1.11.0
* Options added to allow extra information to attached to mrs_data and
fit_result objects as a data frame.
* New functions (combine_fit_XXX) for working with multiple fit results
contained within a list structure.
* Basis set and noise region are now checked for validity in ABfit.
* Added spant_abfit_benchmark function.
* Tentative functions for performing "standard" 1H brain analyses: 
svs_1h_brain_analysis and svs_1h_brain_batch_analysis.
* Improved support for LCModel analyses.

# spant 1.10.0
* Fix for NIfTI MRS reader/writer.
* ortho3 now shows correct labels for orientations other than RAS.
* ortho3_int function renamed to ortho3_inter.
* Argument order change to plot_voi_overlay and plot_voi_overlay_seg to be more
consistent with ortho3.
* Regression fix for partial volume segmentation plotting.
* Echo time parameter is now stored in the meta structure.
* ABfit now performs a 1D phase parameter search before the prefit stage to
improve reliability. May be disabled with the prefit_phase_search fit option.

# spant 1.9.0
* NIfTI MRS reader and writer now uses the header extension for metadata. Thanks
to Jon Clayden for adding extension read/write support to the RNifti package.
* Default plots now have gridlines in the y-direction and the plot line is now
thicker and coloured blue.
* Opacity option added to the plotting functions (alpha).
* Bug fix for comb_coils with SVS data.
* Bug fixes for Siemens geometry information.
* Changed the ordering of arguments to write_mrs and write_mrs_nifti to improve 
consistency with other functions.
* Internal function (ortho3) now used to plot voxel locations on MRI.
* Internal dicom reader function added.
* Tentative support for Siemens and Philips DICOM MRS format added.
* Internal changes to the way orientation information is handled.

# spant 1.8.0
* Added gridplot function.
* New functions added for down sampling.
* Added signal space projection method for MRSI.
* Geometry information is now read from Siemens twix files.
* GitHub actions are now used for continuous integration instead of Travis and
AppVeyor.
* Added precomp function to avoid repeated computation.
* mrs_data2mat function now collapses all dimensions to dynamics by default.
* mrs_data objects now store the nucleus.
* Added a reader for old Varian format (fid/procpar) data.

# spant 1.7.0
* Added write_mrs function which guesses the output format from the file
extension or can be specified as an argument. write_mrs_XXX functions have been
depreciated.
* read_mrs function now tries to guess the format from the file extension.
* Added json sidecar to NIFTI MRS export function.
* Added the option to read MRS data from a NIFTI file and json sidecar using the
read_mrs function.
* Changed default crop_spec region to between 4.0 and 0.2 ppm.

# spant 1.6.0
* Bug fix for GE P file reader.
* Added downsample_mrs function.
* Tentative function (write_mrs_nifti) to write MRS data as a NIFTI format file 
- for evaluation purposes only.

# spant 1.5.0
* Added an option to ABfit to allow the metabolite amplitudes to be negative 
(ahat_calc_method).
* Removed lsei package dependency.

# spant 1.4.0
* Added the option to plot a y = 0 baseline trace for stackplot.mrs_data.
* Added convenience functions to read and write mrs_data to rds format.

# spant 1.3.0
* Added get_fit_table function to combine all fit tables in a fit_result object
into a single dataframe.
* ppm function can now be applied to fit result objects.
* Bug fix for plot_slice_fit_inter and added the option to specify a
denominator.
* Added the option to specify a denominator to plot_slice_fit.

# spant 1.2.1
* Added the option to display a progress bar in fit_mrs function for better
conformance to "Writing R Extensions" in non-interactive use.
* Changed test tolerance to accommodate differences with OSX.

# spant 1.2.0
* Performance improvement for HSVD water filter.
* ABfit unit tests are now run on simulated data to improve consistency between
different platforms.
* Improvements to fit amplitude scaling code.
* Improved checking for mrs_data processing functions.
* Added preprocessing steps vignette.

# spant 1.1.0
* Improved ppm labels for ABfit plot results.
* Bug fix for plot_slice_fit when using fits from masked data.
* Updated unit tests.
* Added vignette on manually adjusting ABfit baseline smoothness.
* Updated the introduction vignette.
* Bug fixes for image and stackplot functions for masked MRS data.
* Bug fix for using RATS with masked MRS data.
* Changes to prepare for for R 4.0.0.

# spant 1.0.0
* ABfit analysis method has been added, and is now default for the mrs_fit
function.
* Added reader for LCModel RAW format data.
* Added read_mri_dyn_dir function for reading dynamic MRS exported from Siemens
scanners.
* Bug fixes for 2D MRSI voxel segmentation calculation.
* Bug fixes for Siemens IMA format reader for SVS data.
* Optional colourbar added to ortho3 function.

# spant 0.19.0
* Added Asc, BHB, Cho, PEth and Ser simulation parameters.
* Added ker option to get_mrsi_voi function.
* Added append_basis function to combine two basis sets objects.
* The align function now accepts more than one reference frequency.

# spant 0.17.0
* Added a function to grid shift 2D MRSI data in the x/y direction.
* Better plotting/fitting support for masking data by setting data points to NA.
* Bug fix for interactive voxel selection position indicator.
* Added mask_xy to mask voxels in a centred rectangular region.
* Minor changes to improve parallel processing support.

# spant 0.16.0
* SNR is now defined as the max data point divided by the standard deviation of
the noise (n.b. factor of two has been removed in-line with upcoming terminology
paper).
* Default rats method improved to work with multidimensional datasets.
* Added norm_mrs function to normalise the intensity of spectral data.
* Added bc_constant function to correct spectral baselines by a constant offset.
* Added re_weighting function to apply a resolution enhancement weighting to the
FID.
* Performance improvement for apodise_xy function.
* sd function now works for mrs_data.
* Added 2D MRSI support for Siemens IMA format.

# spant 0.15.0
* Bug fix for using auto_phase function with a single spectrum.
* Bug fix for comb_coils not returning unaveraged data when requested.
* Added options to combine metabolite signals from the stackplot of a fit object
and adjust the plot margins.
* Added comb_fits function.
* Added collapse_to_dyns function for mrs_fit objects.
* RDA reader now extracts geometry information.

# spant 0.14.0
* Added options to omit basis signals, change label names and combine lipid and
MM signals from the stackplot of a fit object.
* Added auto_phase function for zeroth order phase-correction of simple spectra.
* Added get_subset function to aid MRSI slicing.
* Added decimate_mrs function.
* Added fit_amps function to quickly extract amplitude estimates from a fit
object.
* Bug fix for int_spec function.
* sim_basis function arguments updated to accept acq_par objects.

# spant 0.13.0
* Various bug fixes for Siemens TWIX reader.
* rats and tdsr functions now use the mean spectrum as the default reference.
* Added the option to remove the x axis in an mrs_data plot.
* Added ylim and y_scale options to fit plotting.
* Added %$% operator from magrittr package.
* Added an interpolation option to calc_spec_snr.
* Added hline and vline options to image.mrs_data.

# spant 0.12.0
* Fit results stackplot now has the option to display labels.
* Added the option to reverse eddy current correction.
* Improved GE p-file reader.
* diff function can now be applied to mrs_data objects.
* Complex functions: Re, Im, Mod, Arg and Conj can now be applied to mrs_data 
objects.
* Default simulations for Glc and NAAG have been improved.

# spant 0.11.0
* Added mar argument to plot command.
* td2fd and fd2td now give warnings when used with data already in the target
domain.
* Improved documentation formatting consistency and fixed some spelling errors.
* Added rats method.

# spant 0.10.0
* The names of in-built pulse sequence functions now all start with seq_* to
make them easier to find.
* Added new functions to simulate the following MRS sequences: CPMG, MEGA-PRESS, 
STEAM, sLASER. sLASER sequence kindly contributed by Pierre-Gilles Henry.
* Bug fix for get_mol_names function.
* stackplot function now accepts labels argument and time-domain plotting.
* def_acq_paras function now accepts arguments to override the defaults.
* Added a source field to mol.paras object to cite the origin of the values.
* Option to restore plotting par defaults.
* The magrittr pipe operator is now exported.

# spant 0.9.0
* Updated plotting modes to be one of : "re", "im", "mod" or "arg".
* Updated int_spec function to use "re", "im", or "mod".
* Added a function to replicate data across a particular dimension.
* Added a convenience function to simulate normal looking 1H brain MRS data.
* phase and shift functions now accept vector inputs.

# spant 0.7.0
* Added new function for frequency drift correction.
* Added support for Siemens ima and TWIX SVS data.
* Added support for GE p-file SVS data.
* Added apply_axes fn.
* Support for reading SPM style segmentation results (spm_pve2categorical).

# spant 0.6.0
* Interactive plotting function added for fit results - plot_fit_slice_inter.
* Bug fix for appending dynamic results.
* Bug fix for reading list data files without reference data.
* Bug fix for append_dyns function.
* basis2mrs_data function has been extended to allow the summation of basis
elements and setting of individual amplitudes.
* Added a shift function for manual frequency shift adjustment.
* Added initial unit tests and automated coveralls checking.

# spant 0.5.0
* A default brain PRESS basis is now simulated by the fit_mrs function when the
basis argument isn't specified.
* Added calc_peak_info function for simple singlet analyses.
* crop_spec function now maintains the original frequency scale.
* The basis set used for analyses has now been added to the fit result object.
* Bug fix for simulating basis sets with one element.
* lb function can now be used with basis-set objects.
* Bug fix for spar_sdat reader for non-localised MRS.
* AppVeyor now being used to test Windows compatibility - John Muschelli.

# spant 0.4.0
* Bug fix for SPAR/SDAT SVS voxel dimensions.
* MRSI support added for Philips SPAR/SDAT data.
* Fit plots now default to the full spectral range unless xlim is specified.
* Fit plots allow the x, y, z, coil, dynamic indices to be specified.
* Added the option to subtract the baseline from fit plots.

# spant 0.3.0
* Added stackplot method for fit objects.
* Added functions for registering and visualising SVS volumes on images and 
performing partial volume correction.
* Philips "list data" also now reads noise scans.
* calc_coil_noise_cor, calc_coil_noise_sd functions added to aid coil 
combination.
* Documentation updates for plotting methods.
* Added some simulation methods to userland.

# spant 0.2.0
* Added Siemens RDA format reader.
* Added Philips "list data" format reader.
* Added Bruker paravision format reader.
* Added PROPACK option for HSVD based filtering.
* Added a coil combination function.
* Bug fix for incorrect ppm scale on fit plots when fs != 2000Hz.
* Bug fix for VARPRO analytical jacobian calculation.

# spant 0.1.0
* First public release.
