Changes: - doc: Add definition files for singularity containers with BART - doc: Add documentation of performance options - doc: Add documentation for singularity container - doc: Add documentation for environment variables - affinereg (new): affine registration - bloch (new): Bloch simulation (work-in-progress) - coils (new): simulate coil sensitivity maps - compress (new): compress data using binary mask - cunet (new): conditional U-Net - denoise (new): denoising tool - estmotions (new): non-rigid registration - estscaling (new): estimate a scaling factor from k-space center - gmm (new): Gaussian-Mixture models - grid (new): compute Cartesian grids - grog (new): GROG calibration and gridding (currently only radials) - hist (new): compute histograms - interpolate (new): interpolate and image after transformation - mobasig (sig): forward calculation of physical signal models - multicfl (new): combine/split multi-cfl files - nlinvnet (new): NLINV-Net reconstruction and training - ncalib (new): sensitivity calibration using NLINV - phasepole (new): tool to detect phase poles - pulse (new): compute radio-frequency pulse shapes - raga (new): tool to compute RAGA indices - rovir (new): coil compression with region optimization - sample (new): sample generative score-based models - seq (new): compute MRI sequences - stl (new): read/write STL files - unwrap (new): simply unwrapping tool - tee (new): copy stdin to file and stdout - toraw (new): create raw data files - trajcor (new): retrospectively correct trajectory based on gradient delays - mat2cfl: removed. - bin: zero-fill option - bin: stream support - calc: new function: round - ccapply: realtime geometric coil compression - conway: stream support - copy: stream support - copy: support for reordering of dimensions - epg: make refocusing FA accessible from CLI - ecalib: use Nyström approximation - ecalib: economic mode for 3D coils - fovshift: pass shift as file - invert: option for regularization - join: stream support - mandelbrot: stream support - moba: IR-MECO reconstruction - moba: finalize transparent gpu support in moba - moba: change scaling and command line for T2 moba to be consistent with mobafit - mobafit: CEST fitting - mobafit: simulation based fitting (Bloch + Bloch-McConnell) - nnet: support for nnU-Net for segmenation - nlinv: basis support, temporal regularization, builtin nufft - nlinv: stream support - nufft: fix compatibility to v0.8.00 - pics: use of prox in last iteration of FISTA - pics: (TE-)ASL reconstruction - pics: Euler-Maruyama - reconet: fix compatibility to v0.8.00 - show: support for printing real part and index - signal: enable the input of fat fraction - signal: generating function-based FSE model - signal: buxton model - signal: option to toggle short TR approximation - sim: CEST sequence - traj: option to create RAGA index file - twixread: optional read PMU signal - twixread: read noise scans - rtreco.sh: new script for realtime reconstruction - library: remove divergence free wavelets - library (num): stable and improved random number generation with Philox-4x32 - library (num): GPU support for gaussian random numbers - library (num): rename md_(de)compress -> md_mask_(de)compress - library (num): new functions: md_(z)round(2) functions, md_zsetnanzero(2) - library (num): MPI support for md_copy with strides, and md_zadd2 - library (num): new LAPACK wrappers (svd, eigenvalues, solvers) - library (num): matrix logarithm of upper triangular matrix - library (num): matrix square root of triangular matrix - library (num): complex support for matrix exponentials - library (num): new special functions: Legendre polynomials - library (num): new special functions: simplified hyp2f1 function - library (num): new special functions: approximation of gamma function - library (num): Gauss-Legendre quadrature - library (num): Crank Nicolson - library (num): functions for Gaussian mixture models - library (ismrmd): new functions to parse ismrmrd streams - library (iter): Euler Mayurama - library (linop): shift, slice, hankelization, reshape with flags - library (nn): cast linop to nn - library (nn): support for leaky ReLU - library (nn): normalization layer - library (nn): normalized loss - library (nlops): checkpointing container - general: move to codeberg - general: remove TOOLBOX_PATH and DEBUG_LEVEL (use the new ones with BART_ prefix) - general: stream protocol implementation + tests - general: experimental support for delayed computation - general: Windows DLLs