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New commands: peaksconvert, peakscheck #2918
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cd8bbfb
Created custom callables for different datatypes on cmd
ankitasanil 075db52
Used callable types in commands - mrtrix_cleanup and dwicat
ankitasanil 8d91a38
Changes done as instructed in the review
ankitasanil ebd36cf
Used callable types in few more commands
ankitasanil 2988229
Python API: Integrate argument types across commands
Lestropie 481462f
Changed the syntax as per https://github.com/ankitasanil/mrtrix3/pull…
ankitasanil 54bca48
Python API: Used Python list comprehension as per https://github.com/…
ankitasanil cd33930
population_template: Refine cmdline interface
Lestropie 9f3d624
Change interfaces for robust linear registration estimators
Lestropie 51ccc67
Python API: Updated class names as per https://github.com/ankitasanil…
ankitasanil 47fec95
Modifications in existing code to handle new argument types
ankitasanil b72c211
Modifications in existing code to handle new argument types (contd.)
ankitasanil 6dcfe53
Added inheritance for TracksIn checks as per (https://github.com/anki…
ankitasanil 935a8aa
Python API: Ability to handle piped commands
ankitasanil e749fe9
Changes for output image piping
ankitasanil a830bf4
Python CLI: Tweaks to custom types
Lestropie 4560880
Python CLI: Code cleanup
Lestropie 2894b1d
Move handling of envvar MRTRIX_PRESERVE_TMPFILE
Lestropie 294ea57
Fix pylint warnings for python_cmd_changes branch
Lestropie 70c154e
Python: Move some functions from path to utils module
Lestropie e9393d7
First functional version of image piping with Python scripts
Lestropie 913ce00
mrtrix3.app: Terminate if piping image to stdout
Lestropie 2e1efdb
mrtrix3.app: Improvements to __print_full_usage__ behaviour
Lestropie ff56d40
dwibiascorrect ants: Change command-line options
Lestropie a847938
mrtrix3.app: Fix __print_full_usage__ for subparser algorithms
Lestropie 94abafa
Docs: Improved metavar usage in Python scripts
Lestropie dda5db7
Merge branch 'dev' into python_cmd_changes
Lestropie 1a9759e
dwi2mask consensus: Generalise -algorithm interface
Lestropie a22382f
dwi2mask legacy: Make use of Python command image piping
Lestropie 4208d2e
Initial support for macOS app bundles for GUI apps
bjeurissen ee13d9d
Clean up app bundle generation
bjeurissen 1f846cf
Add macos icons
bjeurissen 17ce416
This should probably be defined when calling cmake instead
bjeurissen dc81d10
Fix typo
bjeurissen 659ebbf
Include application icons with app bundle
bjeurissen 15bb65f
Include file association icons with app bundle
bjeurissen 52f8769
Only add app bundle icons on macos
bjeurissen 7f27e89
Python API: Ranged integers and floats
Lestropie 18e6850
Python: Broad fixing of typed command-line argument usage
Lestropie d511e3d
Python API: Multiple related changes
Lestropie b31c9d9
New unit test for Python CLI typing
Lestropie 7791a38
Fix Python help pages for bound integers & floats
Lestropie 4da90a0
Python API: Multiple API/CLI changes
Lestropie 4c74759
Testing: Verify piped image support for Python scripts
Lestropie ff86c44
Python API: Fix __print_full_usage__ for algorithm wrappers
Lestropie 24f1c32
Fix Python issues identified by latest tests
Lestropie 48d8997
Merge branch 'dev' into cmake_app_bundles
bjeurissen 6778522
Merge remote-tracking branch 'origin/dev' into python_cmd_changes
Lestropie a483d00
Python: Code formatting & documentation regeneration
Lestropie 9822d58
Python CLI: Better metavar handling
Lestropie d158891
clang-format and clang-tidy fixes for #2678
Lestropie d5a4596
Add unit testing of Python CLI
Lestropie 4c331e2
Merge remote-tracking branch 'origin/dev' into python_cmd_changes
Lestropie 9cee5ae
dwicat: Use F-strings
Lestropie d783f8c
population_template: Resolve merge conflicts
Lestropie 55929b0
5ttgen: Algorithms return path of final image to test using 5ttcheck
Lestropie db3ca00
Resolution of pylint errors for #2678
Lestropie ff983de
Python CLI: Fixes to typing & alternative typing interface
Lestropie 553a4fb
Python CLI: Move relevant functions / classes into Parser class
Lestropie e25e977
Fix for population_template for #2678
Lestropie 23f436d
Python API: Fixes to typed CLI
Lestropie 45738a2
Python CLI: Default flags to None
Lestropie 2e6c28a
Merge remote-tracking branch 'origin/dev' into python_cmd_changes
Lestropie e98ecc6
Testing: Finalise Python CLI testing
Lestropie 40b7a7c
population_template: Syntax fixes
Lestropie 8a0d639
Python CLI: Fix for __print_usage_markdown__
Lestropie e384c18
Add argument to specify environment for bash tests
daljit46 7790fd3
testing: Set PYTHONPATH for non-cpp-standalone unit tests
Lestropie d9587e6
Testing: DO not use sed in Python CLI tests
Lestropie 8065803
Testing: Add C++ CLI evaluation
Lestropie be75618
CI: Fix PYTHONPATH setting in MSYS2
Lestropie 08bc526
CI: Fix CLI dunder function checks on MSYS2
Lestropie e014b24
Merge remote-tracking branch 'origin/python_cmd_changes' into fix_pyt…
Lestropie 4c9247b
CI: Fix C++ CLI tests on MSYS2
Lestropie f57bbd8
Merge pull request #2846 from MRtrix3/fix_python_cli_ci_test
Lestropie d6a84ba
CI: Final fixes for addition of C++ CLI tests
Lestropie f458793
Fix compilation of big object files in MINGW debug builds
daljit46 9ce93f3
Merge remote-tracking branch 'origin/dev' into python_cmd_changes
Lestropie 65ba856
Testing: Greater testing of Python image piping support
Lestropie 99dd927
mask2glass: Ensure input image is 3D
Lestropie 7115593
Testing: Verify that Python commands handle paths with whitespaces
Lestropie 4095d76
Testing: Import new test data for new mask2glass tests
Lestropie 05b68d5
Python: Multiple fixes following merge of split tests & CLI changes
Lestropie 69d3590
Merge remote-tracking branch 'origin/dev' into python_cmd_changes
Lestropie 92f9a89
5ttgen hsvs: Fixes to whitespace handling changes
Lestropie fc4b798
population_template: Fix handling of output directory paths
Lestropie f34730d
dwi2mask consensus: Fix for whitespace in scratch directory path
Lestropie 2a55a43
Testing: Whitespaces in scratch directory paths
Lestropie ef5b8c5
mrtrix3.app: Fix argparse exception on existing output filesystem path
Lestropie 40fdc8e
Testing: Fix execution of bash unit tests
Lestropie b3d98c1
Testing: Add comments to CLI tests
Lestropie 4d8f766
Python CLI & testing fixes
Lestropie de5ebe7
Docs: Auto update for changes to -scratch option
MRtrixBot 2eefdcd
Add missing windows.h include header
daljit46 961eeb2
OpenGL: Minimise what is imported by windows.h
Lestropie eac5823
Merge pull request #2914 from MRtrix3/fix_msys2_compilation_minimise_…
Lestropie c2b2e76
Merge branch 'dev' into python_cmd_changes
Lestropie cda68bd
Merge pull request #2678 from MRtrix3/python_cmd_changes
Lestropie a05cef6
Merge remote-tracking branch 'origin/dev' into cmake_app_bundles
daljit46 05d4fa5
New option to build non-core code as a static lib
daljit46 7b01831
Rename MRTRIX_BUILD_STATIC to MRTRIX_BUILD_NON_CORE_STATIC
daljit46 1a015dd
Move cmake/bundle to packaging/macos
daljit46 1eafc83
Add MacOSBundle.cmake module
daljit46 fc07064
New commands: peaksconvert, peakscheck
Lestropie dab9d53
Merge pull request #2897 from MRtrix3/fix_mingw_debug
Lestropie 419ab8f
Add warning if cmake generator is not Ninja
daljit46 a805ef3
Create wrapper scripts for mrview and shview
daljit46 b053f7c
Set CMAKE_OSX_DEPLOYMENT_TARGET for MacOS
daljit46 f4bee41
Set copyright year in MacOSBundle.cmake
daljit46 3c804f6
Set correct icons for mrview
daljit46 399cf16
Merge pull request #2739 from MRtrix3/cmake_app_bundles
bjeurissen 93f3741
Major changes to Python handling following cmake adoption
Lestropie 71bc07c
update_copyright: Changes to reflect post-cmake refactoring
Lestropie 9b3de4d
population_template: Split source code between files
MRtrixBot 6a65e81
git blame: Ignore splitting of population_template code
Lestropie 9ff374b
Avoid using CMAKE_SOURCE_DIR
daljit46 9195a11
Merge pull request #2919 from MRtrix3/generator_warning
daljit46 398cc04
CMakeList.txt: fix very minor typo in warning message
jdtournier 6ca8fd0
Merge pull request #2924 from MRtrix3/cmakelist_typo
daljit46 4e2bc42
Remove app bundle related files and logic now that cmake takes care i…
bjeurissen 2f8df8d
Remove MRTRIX_USE_QT6 as it is no longer supported
bjeurissen 73e4687
Make sure app bundles can find the bundled qt6 plugins
bjeurissen 96ed3f1
remove TIFF from build system following removal from code
jdtournier 648cc08
Merge pull request #2927 from MRtrix3/macos_binary_fixes
bjeurissen 29c8f8d
Merge pull request #2928 from MRtrix3/remove_tiff_from_build
bjeurissen 94cecc2
Bump up OSX_DEPLOYMENT_TARGET to 11.00
bjeurissen 47915bd
Merge pull request #2930 from MRtrix3/ox-deployment-target
bjeurissen 291a747
Cleanup cmake scripts for Python commands
daljit46 70fea8d
Add CMake targets for Python files
daljit46 6f2948a
Change/extend inputs for MakePythonExecutable
daljit46 1f1fb1d
Fix execution of unit tests
daljit46 cee8d41
Fix permissions with CMake < 3.19
daljit46 6424277
Merge pull request #2907 from MRtrix3/build_static
Lestropie f87bc0e
Merge remote-tracking branch 'origin/dev' into cmake_python_changes
Lestropie 3fce648
Fix Python commands, documentation generation, CLI test
Lestropie 561dd2d
Merge pull request #2920 from MRtrix3/cmake_python_changes
daljit46 2c76370
Disable PCHs when building macos release
daljit46 27d377a
Enable MRTRIX_BUILD_NON_CORE_STATIC for releases
daljit46 225f7d7
Merge pull request #2932 from MRtrix3/packaging_changes
daljit46 38cc992
Modified FindFFTW to only look for double precision version of fftw3,…
bjeurissen 8266d9f
Merge pull request #2934 from MRtrix3/fftw_double_only
bjeurissen 07c5290
New command: dirrotate
Lestropie 49f7ede
dirmerge: Better selection of first volume
Lestropie e1f0c99
Add interface library for project-wide compile options
daljit46 79d4edf
Use string_view in dash detection/removal
daljit46 3ab8fd9
Replace union with std::variant for argument choices
daljit46 b0f8018
Use std::string for app CLI
daljit46 6286158
Use std::string in rest of the code
daljit46 54b9672
Cleanup MRView::Window::parse_arguments
daljit46 c21d48d
Store index of args in raw CL input in ParsedArgument
daljit46 f30a90d
Update copyright script with new APP_CPP_STRING
daljit46 11421f3
Fix parsing of arguments in mrcalc
daljit46 4a76d09
Fix command line history string construction
daljit46 32babf0
Remove unnecessary comment
daljit46 5495bbe
Update error message in mrview CLI
daljit46 032fb56
Add further tests for app CLI
daljit46 a6ab4e1
Skip dash tests on MSYS2
daljit46 1f394fb
dwi2tensor: Update reference for constrained fit
Lestropie ac48d3a
Fix warning with GCC14
daljit46 6da0f39
Python API: Support Python 3.12
Lestropie 1f9d3b4
mrtrix3.app: Pylint fixes for 3.12 compatibility
Lestropie 5b5a0ea
mrtrix3.run: Improved shebang parsing
Lestropie 7b10856
Merge pull request #2957 from MRtrix3/python_support_3_12
Lestropie 1a7c2d9
Merge pull request #2956 from MRtrix3/dwi2tensor_constrained_reference
Lestropie 2104608
mrtrix3.run: Further refinement to _shebang()
Lestropie 9c32534
Merge pull request #2950 from MRtrix3/mrtrix-common-target
daljit46 eab106d
ZMerge remote-tracking branch 'origin/dev' into python_shebang_parser
Lestropie d3bb1b4
Merge pull request #2911 from MRtrix3/no_char_arguments
daljit46 fb7d615
run._shebang(): Fix non-use of determined shebang
Lestropie 129bbf5
mrtrix3.run: Some renaming "shebang" -> "interpreter"
Lestropie cd0d42f
Merge pull request #2958 from MRtrix3/python_shebang_parser
Lestropie 5193816
Fix drag & drop on Windows for mrview
daljit46 1f2656d
Parse URLs in GUI drop events using helper function
daljit46 bc57d8d
Move external deps in thirdparty
daljit46 28706ea
Update CI workflows for new handling of external deps
daljit46 47641c8
Patch Eigen configuration with custom patch
daljit46 61aa984
Provide option to specify local dependencies folder
daljit46 fa12bdb
Link pch_cmd against half
daljit46 a4ef4f0
Change location of FETCHCONTENT_BASE_DIR
daljit46 0978325
Use compressed release artefacts rather than cloning repos
daljit46 3014111
Avoid configuring Eigen via FetchContent_MakeAvaiable
daljit46 6736038
Don't set custom FETCHCONTENT_BASE_DIR
daljit46 10c4993
Remove core/file/json.h and core/half.hpp
MRtrixBot d591658
Fix invalid memory access when reading colour maps
daljit46 ab987ea
clang-format-all: Fix shebang
Lestropie f53b197
Merge pull request #2975 from MRtrix3/clang-format-all-shebang
Lestropie a3b583d
Update .git-blame-ignore-devs
MRtrixBot 64e6647
Merge pull request #2976 from MRtrix3/update_git_blame
Lestropie 4f52a59
dirmerge: Code formatting fixes from CI
Lestropie d9ddbd4
Merge pull request #2886 from MRtrix3/fix_drag_drop_mrview_windows
daljit46 02c8a76
Fetch NIfTI headers from remote host
daljit46 b17370c
Remove NIfTI headers from codebase
MRtrixBot c7638ab
CMake: Add NIfTI headers to documentation list of external dependencies
Lestropie 78c8e4a
Remove duplicate line
daljit46 f0f4a4c
Merge pull request #2979 from MRtrix3/remote_nifti_headers
daljit46 f5ec480
5ttgen hsvs: Fix execution where FAST is not available
Lestropie 769a4ca
Merge pull request #2981 from MRtrix3/5ttgen_hsvs_fix
Lestropie abf0985
dwibiasnormmask: Fix masking algorithm selection
Lestropie 7817fda
Merge pull request #2983 from MRtrix3/dwibiasnormmask_maskalgo_fix
Lestropie b6f8d65
dirmerge: New option -firstisfirst
Lestropie a47ed52
New tests for dirmerge command
Lestropie 2a40671
Merge pull request #2944 from MRtrix3/dirmerge_firstvol
Lestropie 1434c49
Fix warnings from new pylint version
Lestropie 025eb0f
Python executables shebang: use env
Lestropie 07693ac
Revisions for new command dirrotate
Lestropie 34f4a83
dirrotate: Reduce default number of rotations evaluated
Lestropie ba814f1
Add tests for dirrotate
Lestropie 5c1f6ec
Merge remote-tracking branch 'origin/dev' into dirrotate
Lestropie f30ab69
Merge pull request #2943 from MRtrix3/dirrotate
Lestropie 2f27ac6
Disable the use of LLD by default
daljit46 153d03c
Use ExternalProject to download test data at build time
daljit46 5fba417
Remove testing data submodules
daljit46 3a7d2f7
Update commit hashes for testing data repos
daljit46 91ac695
Log location of local testing data directories
daljit46 de81d47
Disable download logs for NIfTI headers to the console
daljit46 7bd2a1d
dwibiasnormmask minor tweaks
Lestropie 0b27783
responsemean: Fix terminal message for 1 b-value
Lestropie ad3f5b6
Download NIfTI headers from GitHub
daljit46 bb38d56
Merge pull request #2993 from MRtrix3/fix_nifti_download
bjeurissen 45e3d96
Merge pull request #2848 from MRtrix3/remove_data_submodule
daljit46 39d61f8
Merge pull request #2989 from MRtrix3/mrtrix_use_lld_option
daljit46 81d10ef
peaksconvert: Fix compilation
Lestropie 68aa74b
Merge remote-tracking branch 'origin/dev' into new_peaks_cmds
Lestropie 9939209
peaksconvert: Resolutions following merge
Lestropie 19176e9
mrcalc: Support -config option
Lestropie 22178a1
peakscheck: Updates following merge
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peaksconvert: Fix compilation
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -71,7 +71,7 @@ void usage() { | |
| + Argument("choice").type_choice(formats) | ||
| + Option ("out_reference", "specify the reference axes against which the output directions will be specified" | ||
| " (defaults to real / scanner space if omitted)") | ||
| + Argument("choice").type_choice(references) | ||
| + Argument("choice").type_choice(references); | ||
|
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. warning: do not implicitly decay an array into a pointer; consider using gsl::array_view or an explicit cast instead [cppcoreguidelines-pro-bounds-array-to-pointer-decay] + Argument("choice").type_choice(references);
^ |
||
| // TODO Implement -fill | ||
| //+ Option ("fill", "specify value to be inserted into output image in the absence of valid information") | ||
| // + Argument("value").type_float(); | ||
|
|
||
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warning: do not implicitly decay an array into a pointer; consider using gsl::array_view or an explicit cast instead [cppcoreguidelines-pro-bounds-array-to-pointer-decay]
+ Argument("choice").type_choice(formats) ^