RF: Remove "using namespace std". Any issues should be fixed downstream
MNT: version
DOC: changelog
TEST: add pyfeeds test
DOC: changelog
MNT: Clear arma_aligned flags to avoid struct padding issues
CI: no longer test older than c++11
TEST: new armadillo requires minimum c++11
DOC: changelog, readme, armadillo license/notices
MNT: Updated to armadillo 10.5.1
MNT: add common test stage
MNT: Tweak tests to enable out-of-source compliation/execution
MNT: Don't assume specific compiler executable names
TEST: Fix failed merge
CI: Integrate common fsl/fsl-ci-rules into .gitlab-ci.yml pipelines (auto-generated fsl-ci-rules)
MNT: Update install targets
MNT: Version
DOC: Update usage
TEST: Adjust compile flags+include paths
MNT: Re-arrange header files
MNT: use GLOBALHFILES to install armadillo
MNT: remove depend file
RF: HFILES, not HDRFILES; other cosmetic tweaks
DOC: readme updates
MNT: FSL makefile for armawrap - depends on adjusted FSL makefile machinery in new base project
TEST: Can't call a global "data" in c++17
CI: test with/out optimisation
TEST: same randomness when compiling direct against armadillo
MNT: Explicitly mark destructor as noexcept(false) in c++>=11
RF: Explicitly cast to int, rather than changing type, to avoid other complaints
TEST: mistake in lcov alias
TEST: set default compiler
CI: Test different C++ standards
TEST: Adjustments so that env-provided CXXFLAGS will be used by default, but can be overridden. Also use env-provided GCOV if specified
MNT: version
DOC: changelog
BF: Fix bug in subview_assign - "-diag" was wrapping around because diag is an unsigned int. Only seems to occur when using -std newer than c++98
TEST: fix usage of ARMAWRAP_INCLUDE_DIR
DOC: changelog
MNT: version
RF: Adjust NEWMAT::SVD to explicitly fail if passed a matrix with less rows than columns (for compatibility with newmat behavuiour). Remove U truncation, as arma::svd_econ does it for us (whereas arma::svd does not)
TEST: Test to make sure SVD works with non-square matrices, and fails for MxN matrices where M < N. Minor adjustments to test runner
fsl-avwutils 2209.0 2101.0 --> 2209.0
MNT: Removed the segment option from options object
MNT: Removed segment option
MNT: Moved NN interpolate to newimage library
ENH: Euclidean Distance Transform
Add dog edges
ENH: Zero s/q forms after swap if unset
BF: Force zero transforms for -deleteorient
MNT: Clarify *thrP usage
MNT: Don't assume namespaces included by external headers
MNT: Clean up makefile
MNT: include nemat -> include armawrap/newmat
MNT: include cprob/libprob.h, rather than libprob.h directly
RF: Skip file name, in case it contains e.g., "dim2"
MNT: Handle paths with spaces in their names
fsl-basisfield 2203.1 1910.0 --> 2203.1
TEST: update for new SplineField constructor (requires NoOfThreads instance)
Added a vectorised Get(vec) for getting field and/or derivatives in one call
Now uses Utilities::NoOfThreads for constructors
TEST: remove unnecessary libs from ldflags
TEST:macOS/M1 benchmarks
TEST: parity between feedsRun and cpp names
TEST: macOS-64 benchmarks
MNT: Make sure string returned by ::what is not a temporary
TEST: linux benchmark files
TEST: feedsRun script, allow RNG seed to be specified
TEST: Jesper's splinefield tests. Need to rework a little bit
Added functionality to set and check for number of threads
Made sure that nthreads was passed from splinefield to any SpMat or BFMatrix that it returns
BF: Missing initialiser from splinefield copy constructor. No effect in C++11, but was causing problems in C++17
RF: Replace boost::shared_ptr with std::shared_pointer, disambiguate some function calls
RF: Disambiguate symbols from MISCMATHS
MNT: Shared lib dependencies must be specified when compiling a shared lib on macOS
MNT: Clean up makefile
MNT: Fix newmat include path
STY: Whitespace
Fixed bug that meant parallel version wasn't actually used for Bending energy Hessian
Parallelised a subset of functions in splinefield class
BF: Fix accidental down-casting of unsigned int to int
fsl-baycest 2111.0 FSL6-0-1 --> 2111.0
Merge branch 'mnt/conda' into 'master'
MNT: clean up makefile
fsl-bet2 2111.0 2103.0 --> 2111.0
MNT: Don't assume any namespaces are included by external header files
MNT: clean up makefile, shared lib renames
fsl-bianca 2209.2 2106.0 --> 2209.2
BF: Debug binary location left in
MNT: Changes for new distancemap
BF: use bash not sh
BF: Rename cluster -> fsl-cluster
fsl-bint 2111.0 FSL6-0-0 --> 2111.0
Merge branch 'mnt/conda' into 'master'
MNT: More namespacing
MNT: Remove "using namespace" statements from header files
MNT: Shared lib dependencies must be specified when compiling a shared lib on macOS
MNT: clean up make file, shared lib renames
fsl-cluster 2201.0 2004.0 --> 2201.0
MNT: rename cluster to fsl-cluster to avoid naming conflicts with third party packages. A wrapper script called "cluster" will still be installed, for legacy compatibility
MNT: Don't assume any namespaces are included by external header files
MNT: Clean up makefile, update shared lib names
MNT: include cprob/libprob.h rather than libprob.h
fsl-cprob 2111.0 2006.0 --> 2111.0
MNT: Don't declare extern INFINITY
MNT: return values
RF: We want to keep these definitions - they should only be undefined if compiling on super super old systems which don't support nan/inf
RF: Alternative mtherr function which doesn't print anything
MNT: true_gamma - alias for gamma, used by fabber_models_dsc
DOC: readme
MNT; Dis-ambiguate usage of gamma function
RF: Use unique CPROB namespace, and isolate MISCMATHS namespace import hack to libprob.h
RF: Compile as C++ lib
RF: Refactor to compile as C++ library: - Rename .c to .cc - Rework legacy "void func(a) double a {..}" function signatures - Put everything in MISCMATHS namespace in both obj and header files (will change this shortly) - Do not use extern - include and instead - Do not define INFINITY/NAN globals - use those from instead
MNT: macOS requires all shared lib dependencies to be specified when compiling a shared lib; don't specify -lfsl-cprob when compiling libfsl-cprob
BF: typo in makefile
MNT: Update makefile to compile shared, not static library
fsl-data_standard 2208.0 2006.0 --> 2208.0
MNT: Fix some sform/qform codes. Fix lowercingulum affines and codes, and remove non-printable characters from aux_file field.
fsl-eddy 2111.0 2106.1 --> 2111.0
RF: Use new CUDACXXFLAGS for compiling .cpp files to be linked into eddy_cuda, so we can pass same compiler flags
RF: Use g++ to compile .cpp code, and only use nvcc for .cu files and final linkage. This is because we may want to use different C++ standards for g++-compiled and nvcc-compiled code (c++17 for former, c++14 for latter).
BF: Make sure build dirs are created
RF: Rename eddy_openmp -> eddy_cpu
RF: Rename "eddy_openmp" to "eddy_cpu", in anticipation of replacing openmp with std::thread. Add -rdynamic so that fsl/utils/stack_dump.h works. Add explicit build dependencies for CUDA object files to reduce compilation times during development.
MNT: Not building eddy_cpu
MNT: Don't build single threaddy
MNT: Don't use EddyTry/EddyCatch macros on destructors, as they default to noexcept in C++>=11
MNT: Namespace disambiguation in CUDA code
MNT: Namespace disambiguation of vraious symbols. Use std::shared_ptr instead of boost::shared_ptr
BF: cudabasisfield added to LIBS, so being included in non-CUDA builds
BF: improper use of os.execv - need to pass command name as first argument
RF: Link against cudaver-specific cudabasisfield solib
MNT: Save nvcc object files to CUDA_VER-specific build directory
MNT: don't delete wrapper script on make clean
MNT: Port eddy wrapper script to python, for improved portability and cleaner code
RF: Compile statically linked, and labelled eddy_cuda binaries - CUDA toolkit libraries are statically linked (depends on fsl/base 2107.0), and eddy_cuda binaries are named eddy_cudaX.Y
MNT: new EddyCudaHelperFunctions.cu and CPUStackResampler.cpp files
ENH: wrapper script to call eddy_cuda/eddy_openmp/eddy_cpu
MNT: Fix cudabasisfield #include
RF: Put cuda obj files in separate build dir, because there are name overlaps (the reason why original Makefile renamed cuda files to %_cuda.o)
BF: openmp objs were being constructed incorrectly
BF: Separate out CPU from CUDA objects - probably an artifact of shared lib experimentation
BF: No longer building shared libs
RF: I misunderstood the structure of eddy - cannot use separate shared libs, as there are circular dependencies between eddy.cpp and other files.
RF: No longer naming binaries with cuda version. Compile eddy_cuda executable with nvcc
MNT: note about compilation
MNT: -fopenmp in final link
MNT: fix eddy libs
MNT: Clean up makefile
MNT: Fix newmat/cprob include paths
STY: whitespace
fsl-fast4 2111.0 FSL6-0-0 --> 2111.0
Merge branch 'mnt/conda' into 'master'
MNT: Remove "using namespace" statements from headers, don't assume namespaces included by external headers
MNT: clean up makefile, shared lib renames
fsl-fdt 2202.5 2103.0 --> 2202.5
BF: fix argument parsing
BF: Remove LD_LIBRARY_PATH as breaking script on cluster
RF: Change Makefile so that gpu build only compiles/installs CUDA binaries. Everything else is done via cpu build
BF: shared lib name has changed
MNT: xfibres_gpu wrapper script which identifies the installed CUDA versino and calls an appropriate xfibres_gpuX.Y executable
MNT: xfibres_gpu and libfsl-bedpostx_cuda.so are labelled with the CUDA version they were compiled against
MNT: Need to include thrust/[host|device]_vector
MNT: Don't assume any namespaces are included by external header files
MNT: Don't assume any namespaces are included by external header files. More to come
MNT: Replace boost::shared_ptr with std::shared_ptr.
MNT: -lcuda / -lcudart handled automatically
RF: Use nvcc for compilation of xfibres_gpu, so that nvcc-specific flags and libs are applied
MNT: Clean up build control - the cpu/gpu flags can be used to build the CPU and/or the GPU bits. Default behaviour is to build CPU bits only.
RF: use "gpu" rather than "FDT_COMPILE_GPU"
MNT: rename nvcc flags
MNT: nvcc needs link options when compiling shared library
MNT: clean up makefile; GPU compilation is now controlled via FDT_COMPILE_GPU variable
MNT,STY: fix newmat/cuda include paths, whitespace
STY: whitespace
MNT: Include cprob/libprob.h rather than libprob.h
fsl-feat5 2201.2 2104.0 --> 2201.2
BF: Change copyright hook
RF,BF: MAke sure JS callbacks are are accessible by other frames. Use iframe instead of frame. Suppress server log messages
RF,BF: Copy js lib files into pnm output dir. Fix a few bugs in pnm_stage1. Keep web server running for a few secs to give browser enough time to load PNM report page
RF: Re-write pnm_stage1 in python. Automatically start a local web server, and open PNM report in web browser from that server, to prevent CORS errors
MNT: Defer javascript execution until page has loaded
MNT: Use DATAFILES variable to install flobs/pnm data
MNT: Add PNM html files (moved over from base project)
RF: Feat is going to have a $FSLDIR/data/feat5/ directory - may as well store default_flobs.flobs files in there
BF: Rename cluster -> fsl-cluster
MNT: Don't assume any namespaces are included by external header files
MNT: Dependencies need to be specified when compiling a shared lib on macos
MNT: clean up makefile
MNT: include cprob/libprob.h rather than libprob.h
fsl-film 2111.0 2007.0 --> 2111.0
MNT: Don't assume any namespaces are included by external header files
MNT: Shared lib dependencies must be specified when compiling a shared lib on macOS
MNT: Fix newmat include paths
STY: whitespace
MNT: fix newmat include paths
STY: whitespace
MNT: clean up makefile, shared lib renames
MNT: include cprob/libprob.h rather than libprob.h
fsl-filmbabe 2111.0 FSL6-0-0 --> 2111.0
Merge branch 'mnt/conda' into 'master'
MNT: Don't assume any namespaces are included by external header files
MNT: fix newmat include paths
STY: Whitespace
MNT: clean up makefile, shared lib renames
MNT: include cprob/libprob.h rather than libprob.h
fsl-first 2203.0 2006.0 --> 2203.0
RF: Change first3Dview to use fsleyes instead of fslview
BF: Rename cluster -> fsl-cluster
MNT: Don't assume any namespaces are included by external header files
MNT: clean up makefile, shared lib renames
fsl-first_lib 2111.0 FSL6-0-0 --> 2111.0
Merge branch 'mnt/conda' into 'master'
MNT: Don't assume any namespaces have been included
MNT: Error in LIBS declaration
MNT: Shared lib dependencies must be specified when compiling a shared lib on macOS
MNT: clean up makefile, compile shared not static
MNT: fix newmat include path
STY: whitespace
fsl-flameo 2111.0 FSL6-0-0 --> 2111.0
Merge branch 'mnt/conda' into 'master'
MNT: Remove "using namespace" statements from header files, don't assume namespaces included from external headers
MNT: CiftiLib needs special handling
MNT: fix newmat/cifti include paths
STY: whitespace
MNT: clean up makefile, shared lib renames
MNT: include cprob/libprob.h rather than libprob.h
fsl-flirt 2111.0 2108.0 --> 2111.0
MNT: Don't assume any namespaces included by external header files
MNT: need meshclass
MNT: fix newmat include path
STY: Whitespace
MNT: Clean up makefile, shared lib renames
fsl-fnirt 2203.0 FSL6-0-0 --> 2203.0
MNT: Remove unnecssary boost namespace - should have been removed in migration from boost::shared_ptr to std::shared_ptr
MNT: Rename new_invwarp to invwarp (see related changes in fsl/fugue, removing the old invwarp)
MNT: Replace boost::shared_ptr with std::shared_ptr. Don't assume any namespaces are included by external header files
MNT: Need cprob
MNT: fix newmat include paths
STY: Whitespace
MNT: Clean up make files, shared lib renames
Makefile now uses c++11 to build. And changes brought about by that (explicit casts).
BF: Address compiler errors about implicit cast from int to Real (a.k.a double)
BF: typo
BF: Avoid implicit downcast from int64_t to int
fsl-fugue 2201.2 2010.0 --> 2201.2
RF: Don't fail if sform/qform don't match. Use newimagevox2mm_mat instead, which will follow the convention of using sform if sform code !=0, or qform if qform code !=0, or fall back scaling affine
DOC: Mention default value for interp in cli help
MNT: Remove old invwarp - new_invwarp (in the fnirt project) has been in use for over 10 years now
MNT: EXPOSE_TREACHEROUS needed for warpfns
MNT: Replace boost::shared_ptr with std::shared_ptr. Don't assume any namespaces are included by external header files
MNT: Need cprob
MNT: Clean up makefile, shared library renames
MNT: Fix newmat include paths
STY: Whitespace
fsl-giftiio 2111.0 FSL6-0-0 --> 2111.0
Merge branch 'mnt/conda' into 'master'
MNT: Shared lib dependencies must be specified when compiling a shared lib on macOS
MNT: use shared lib
MNT: clean up makefile
Merge branch 'mnt/rmeove-have-zlib' into 'master'
MNT: Remove all uses of HAVE_ZLIB
fsl-gps 2111.0 FSL6-0-0 --> 2111.0
Merge branch 'mnt/conda' into 'master'
MNT: Replace boost::shared_ptr with std::shared_ptr. Don't assume any namespaces are included by external header files
MNT: clean up makefile
MNT: fix newmat includes
STY: Whitespace
fsl-lesions 2111.0 2104.0 --> 2111.0
MNT: Don't assume namespaces included by external header files
MNT: clean up makefile
fsl-libgdc 2111.0 2006.0 --> 2111.0
BF: Seems like on macOS, other shared libraries need to be specified when compiling a shared lib?
MNT: compile shared, not static
fsl-libmeshutils 2111.0 FSL6-0-0 --> 2111.0
Merge branch 'mnt/conda' into 'master'
MNT: Don't assume any namespaces are included by external header files
MNT: Shared lib dependencies must be specified when compiling a shared lib on macOS
MNT: clean up makefile, shared lib renames
MNT: include cprob/libprob.h rather than libprob.h
fsl-libvis 2111.0 1909.0 --> 2111.0
MNT: Fix executable rule (shared lib files were being passed)
MNT: Don't assume that any namespaces are available
MNT: Don't specify -l when compiling
MNT: Shared lib dependencies must be specified when compiling a shared lib on macOS
MNT: poke libs, make sure shared libs are built before executables
MNT: fix libvis (now local) include paths
STY: whitespace
RF: Move many utilities from miscvis into libvis, to resolve circular dependencies
MNT: Compile shared, not static library
MNT: Fix includes
fsl-mcflirt 2111.0 FSL6-0-1 --> 2111.0
Merge branch 'mnt/conda' into 'master'
MNT: Don't assume namespcaes included by external headers
MNT: cruft
MNT: fix newmat include path
STY: whitespace
MNT: clean up makefile, shared lib rename
fsl-melodic 2111.1 2012.0 --> 2111.1
MNT: Use std::shuffle instead of std::random_shuffle, which has been removed in C++17
MNT: Remove "using namespace" statements from headers, don't assume namespaces included in external headers
MNT: Shared lib dependencies must be specified when compiling a shared lib on macOS
MNT: Actually use local version of zeropad
STY; whitespace
MNT: bwtf no longer exists
MNT: Use a namespace to avoid conflicts with common names (e.g. "data")
STY: Whitespace
MNT: Use a namespace, as there are other things in the world called "data", "glm", etc etc.
STY: whitespace
MNT: Remove stupid dependency on fdt
MNT: clean up makefile
MNT: fix newmat/cifti include paths
STY: whitespace
MNT: include cprob/libprob.h rather than libprob.h
fsl-meshclass 2111.0 2102.0 --> 2111.0
MNT: Need LDFLAGS to compile shared libs on macOS
MNT: More namespace disambiguation
MNT: Remove "using namespace" statements from header files
MNT: Clean up makefile
fsl-misc_c 2111.0 2106.0 --> 2111.0
MNT: Put ztop_function in a namespace. Remove "using namespace" statements from header files
TEST: make feedsRun executable
MNT: Clean up makefile
MNT: Include cprob/libprob.h instead of libprob.h. Clean up some cruft in makefile
fsl-misc_scripts 2111.0 2004.0 --> 2111.0
Merge branch 'mnt/conda' into 'master'
MNT: Text2Vest, Vest2Text, fsl_abspath are provided by fslpy
MNT: clean up makefile
fsl-misc_tcl 2206.0 2010.0 --> 2206.0
MNT: Search for $FSLDIR/bin/fsleyes, not $FSLDIR/bin/fslview
ENH: Allow global scaling of fsl_sub runtimes
BF: Allow for fslversion not being present
MNT: Added tcl symbols for internal projects
MNT: Install a "master" pre-generated tclIndex, rather than using auto_mkindex whenever each TCL project is installed.
MNT: migrate fslio.tcl from defunct fslio project
BF: Typo
MNT: Runtcl is now part of fsl-base. Makefile uses built-in rules
MNT: minor cosmetic changes
BF: Fix for very intermittent can't read ::errorCode: no such variable bug
fsl-miscmaths 2203.2 2010.0 --> 2203.2
MNT: Use newmat rather than armadillo method
BF: Replace problematic rotmat->quaternion routine with call-out to more robust, pre-existing niftio routine
Added some std:: to make sure right numeric functions called.
Changed constructors to take Utilities::NoOfThreads instead of unsigned int
Changed nthr to NoOfThreads in splinterpolator constructor
BF: Invalidate splines on a change in spline order
MNT: renamed final instances
MNT: renamed variable
BF: Spline validity
Added method save_volume_and_splines to write a volume along with its spline coefficients
fsl-newmesh 2111.0 1904.0 --> 2111.0
RF,MNT: Replace boost::shared_ptr with std::shared_ptr. Do not assume any namespaces have been included
MNT: Missing library needed for linking on macOS
MNT: error in LDFLAGS
MNT: Shared lib dependencies must be specified when compiling a shared lib on macOS
MNT: nifti constants are now in NiftiIO namespace
STY: whitespace
MNT: fix newmat include paths
STY: whitespace
MNT: clean up makefile, compile shared not static
fsl-newran 2111.0 FSL6-0-0 --> 2111.0
Merge branch 'mnt/conda' into 'master'
MNT: Add link flags when compiling so file
Merge branch 'mnt/conda' into 'master'
MNT: Add link flags when compiling so file
MNT: Need include statement
RF: Remove "using namespace" statements from header files
MNT: rename to libfsl-newran.so
MNT: Compile shared library, not static library
fsl-possum 2111.2 FSL6-0-0 --> 2111.2
Merge branch 'mnt/register' into 'master'
MNT: Remove uses of register keyword (disallowed in c++17)
Merge branch 'mnt/conda' into 'master'
MNT: Don't assume any namespaces are included by external header files
BF: Can't use numeric operators on booleans
STY: whitespace
MNT: fix newmat includes
STY: whitespace
MNT: Clean up makefile
MNT: include cprob/libprob.h rather than libprob.h
Merge branch 'paulmc-master-patch-68773' into 'master'
MNT: Don't manipulate [DY]LD_LIBRARY_PATH
fsl-ptx2 2111.4 2101.1 --> 2111.4
BF: Fix creation of seed->target affine in probtrackx2_gpu --omatrix2. Was previously assuming that target was defined in diffusion, not seed, space.
RF: Size checks when stripping suffixes, bail if filestream is not good
BF: Re-write/clean up code which generates names for target masks. Previous logic was flawed, and could result in tmpname[-1] = '_';
RF: Change Makefile so that gpu=1 build only compiles/installs CUDA binary
MNT: wrapper script to find+execute a suitable version of probtrackx2_gpu
MNT: label probtrackx2_gpu binary with the CUDA version it was compiled against
MNT: need EXPOSE_TREACHEROUS
MNT: Don't assume any namespaces are included by external header files
MNT: Compile probtrackx_gpu.o with nvcc
MNT: cudadevrt handled automatically
RF: Remove profiling calls (and hence remove dependence on libnvToolsExt)
MNT: whitespace
RF: Remove cudart/cuda (they are added autimatically), and intending to remove reliance on nvToolsExt
RF: Allow conditional compilation of either CPU bits, or GPU bits, or both
RF: Use "gpu" rather than "PTX2_COMPILE_GPU"
MNT: rename nvcc flags
MNT: Clean up makefile
MNT: Disambiguate round function
STY: whitespace
use long to avoid overflow in num_threads
fsl-qboot 2111.0 2010.0 --> 2111.0
MNT: Don't assume any namespaces are included by external header files
MNT: clean up makefile
fsl-randomise 2203.2 2101.0 --> 2203.2
BF: short is too short to support NIFTI-2 lengths
BF: combineScript uses bash-isms
BF: inclusive to match older range
ENH: Small p-values are no longer truncated, plus masking on thresholded output
Plausable fix for underflow and masking problems
MNT: URBG for C++17
MNT: URBG for C++17
MNT: Don't assume any namespaces are included by external header files
MNT: clean up makefile, shared lib renames
MNT: include cprob/libprob.h rather than libprob.h
fsl-relax 2111.0 2007.0 --> 2111.0
Merge branch 'mnt/conda' into 'master'
BF: Wrong include path
MNT: clean up makefile
MNT: Fix includes
STY: whitespace
fsl-siena 2111.0 2006.0 --> 2111.0
MNT: Don't assume any namespaces are included by external header files
MNT: clean up makefile
STY: whitespace
fsl-slicetimer 2111.0 FSL6-0-0 --> 2111.0
Merge branch 'mnt/conda' into 'master'
MNT: Don't assume any namespaces included by external headers
MNT: fix newmat include paths
STY: whitespace
MNT: clean up makefile
fsl-susan 2111.0 FSL6-0-0 --> 2111.0
Merge branch 'mnt/conda' into 'master'
MNT: Don't assume any namespaces are included by external headers
MNT: susan needs cprob
MNT: Clean up makefile, shared lib renames
fsl-swe v1.1.0 v1.0.3 --> v1.1.0
Merge branch 'mnt/conda' into 'master'
RF: Don't assume any namespaces have been included by external headers
MNT: Shared lib dependencies must be specified when compiling a shared lib on macOS, don't specify -lfsl-swe when compiling libfsl-swe.so
MNT: clean up makefile
MNT: include cprob/libprob.h rather than libprob.h
fsl-tbss 2111.0 2101.0 --> 2111.0
Merge branch 'mnt/conda' into 'master'
MNT: Don't assume any namespaces are included by external header files
MNT: Clean up makefile, shared lib renames
fsl-topup 2203.1 1911.0 --> 2203.1
RF: Moved blas threading control to utils
Added call to Utilities::fsl_init_blas_threading() to disable BLAS multi-threading
Various refactorings aimed at speed ups
Added _nthr to TopupScan and TopupScanManager
Added _nthr to TopupCF and to construction of splinefield
Added --nthr command line argument
Added a function level try-catch on main
Changed exception classes to avoid compiler warnings
MNT: Replace boost::shared_ptr with std::shared_ptr. Don't assume any namespaces are included by external header files
MNT: Shared lib dependencies must be specified when compiling a shared lib on macOS
MNT: Compile a shared library for topup, so eddy don't have to recomple topup files
BF: typo
MNT: clean up makefile
MNT: fix newmat include paths
STY: whitespace
Changed default datatype of output from same as input to float. If one wants to preserve input type one must now use --datatype=preserve
Added -std=c++11 to USRCXXFLAGS
fsl-utils 2203.2 2007.0 --> 2203.2
MNT: use local threading.h
RF: superfluous __attribute__
DOC: Spelling mistake
RF: Removed debug text
RF: Rename to indicate general scope
RF: Global object for setting threading parameters
ENH: Prototype global options code
RF: Need to load libblas.dylib on macOS
MNT: Check for invalid key in EndAccumulate, small tweaks to threading_init
ENH,BF: Remove call to no-longer-existing CreateAccumulate function. New fsl_init_blas_threading function, which can be called to disable BLAS threading in an implementation-independent way.
STY: use of reference operator
STY: whitespace
ENH: Accumulate methods, for timimg repeat execution of code blocks
ENH: Singleton/default FSLProfiler, handy if you want to direct all profiling outputs to a single file.
Minor formatting
Fixed X_OptionError to avoid compiler warning
First commit of a file where we can collect utilities related to threading
Fixed FSLProfilerException so it doesn't cause compiler warning
MNT: Update stack_dump.h to work on apple M1
STY: whitespace
MNT: More namespacing
RF: Disambiguate Tracer
RF: Remove "using namespace" statements from header files
MNT: Shared lib dependencies must be specified when compiling a shared lib on macOS
BF: Dodgy indentation, and not enough braces
STY: Whitespace
RF: Conformance with C++17
MNT: use CXX, not CXX11
MNT: Update makefile to new make system, and to build shared library
MNT: Fix newmat includes
fsl-warpfns 2203.0 2106.0 --> 2203.0
Added a deffield2jac function for when displacements are 1D
Changed nthr to Utilities::NoOfThreads everywhere
BF: Make nthr optional in main raw_general_transform function
raw_general_transform, and all interfaces to it, now takes nthr as an optional parameter. It has been extensively tested
Added path to build test_parallel_warpfns
There is now a parallel, but untested, version of raw_general_transform
Fixed exception classes to not return address of temporary objet
Starting to rewrite raw_general_transform for parallelisation
MNT: Disambiguate Max function
RF,MNT: Replace usage of boost::shared_ptr with std::shared_ptr. Don't assume any namespaces are included by external header files.
MNT: Wrong shared lib name
MNT: Shared lib dependencies must be specified when compiling a shared lib on macOS
MNT: Shared lib dependencies must be specified when compiling a shared lib on macOS
MNT: fix newmat include path
STY: whitespace
MNT: Clean up makefile
fsl-xtract_data 1.3.4 1.3.2 --> 1.3.4
Updated AF protocols to include ordered targets.
Update do_reg_F99.sh
Updated default xtract_data path
fsl-znzlib 2111.0 FSL6-0-0 --> 2111.0
Merge branch 'mnt/conda' into 'master'
MNT: don't add -lfsl-znz to LDFLAGS for its own compilation, only for testprog
MNT: Shared lib dependencies must be specified when compiling a shared lib on macOS
MNT: Clean up makefile, compile shared, not static library
Merge branch 'mnt/remove-have-zlib' into 'master'
MNT: Remove HAVE_ZLIB and HAVE_FDOPEN switch. The latter is not used by anything, and the former is never unset.