New qa fast pr #370
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New qa fast pr #370
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Wilson Tang
Update NDD/ndmg Fork Staging Branch
Update NDD/ndmg Fork deploy from upstream
loftusa
reviewed
Dec 13, 2019
loftusa
reviewed
Dec 13, 2019
loftusa
reviewed
Dec 13, 2019
Lawreros
requested changes
Dec 13, 2019
|
Looks good, if you edit your tutorial with what I suggested then I think this is ready to merge |
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@JialinKang Sorry, one more thing. Could you edit the tutorial filename to not include spaces? Spaces cause all sorts of problems a lot of the time. Use |
Lawreros
requested changes
Dec 13, 2019
Lawreros
approved these changes
Dec 14, 2019
loftusa
approved these changes
Dec 14, 2019
Lawreros
added a commit
that referenced
this pull request
Feb 12, 2020
* Doc revision (#302) * added for-loop * Added documentation * lawreros@gmail.com * Added documentation * Added documentation and removed useless functions * fixed init * Added documentation and fixed s3 issue * fix * Delete multigraph_pipeline.py Not used in ndmg * Update ndmg_bids.py Streamlined for-loop * Update gen_utils.py * Update ndmg_bids.py * Dmri reg (#304) * add _.ipynb to gitignore * change name of dmri_reg to DmriReg * change names to be more clear * better print statement, name changes * make naming convention more clear * rename preproc * add print statement * purge the rest of the dmri_reg references * write dope decorator, add it to everything in reg_utils * fixed issue with import changes * Revert "write dope decorator, add it to everything in reg_utils" This reverts commit a3b8047. * fixed misnamed function * gen_reg change test * fix * Added skull parameter * fixed stupid mistake * Update ndmg_bids.py * Update gen_reg.py * Update reg_utils.py * added key-error function * added file renaming * test * test * test * add comands run inside docker container * test * added missing "done" * docker copy * directory update * directory update * Update reg_utils.py * aws testrun key encryption aws key update test s3 change branch addition test str change one last shot New approach fix docker error fix typos re-encryption test encrypt_test s3 fix push connectome data Added branch and commit information reorganize Fold check Formatting check switch back travis fix line deletion echo deletion * travis_fold test * foldv2 * html addition * Dipy newversion (#311) * initial dependency fix * fix up dipy imports in gen_track * organize imports in gen_track * rename all classifiers, add some TODOs * many renames * iterrated through everything but EudXDirectionGetter * fix gen_graph error * fix dsn * fix bug in dsn * native_dsn is totally fixed now * add clearer print statements * write dope decorator, add to a bunch of functions in gen_utils * fix merge conflict * fiddling with check_exists arguments a bit * functions get displayed with check_exists, so removing print statements * remove mni space for now. Fix before merge into deploy. * clearer decorator * remove some old func code * remove mni from travis * remove comment * fix graph saving * no check_exists on skullstrip_check * check for TypeError in check_exists * format fix * Remove non-html * Removed git lfs neuroparc * black on all files * change mgu to gen_utils * simplify get_filename, delete extra function * remove fmri func * remove extract_mask * remove bet skullstrip function * remove reslice_to_xmm, not used * remove get_sphere, as we use the dipy func instead * remove function from name_resource, change mgu naming conventions * remove unecessary methods from gen_graph * remove get_status from ndmg_cloud, unecessary function * organize imports across ndmg * black on all files (#319) * Update Dockerfile * Update .travis.yml * change class naming syntax for all classes * rename more classes, change module name * s3_utils to cloud_utils everywhere * Revert "Travis deploy" * BREAK THE WORLD AND PURGE EVERYTHING, CHAOTIC GOOD, ENTIRE MODULE ORGANIZATION CHANGED * Push travis output to s3 bucket * remove script that wasnt doing anything * merge conflict in setup.py * fix merge conflicts * the world is currently on fire, but will soon be reborn anew, like a phoenix * ndmg now pip installs again * add functools.wraps to check_exists, add ndmg_bids as a backwards-compatibilty option to setup.py * add proper imports * some missing imports in dwi_pipeline * finish organizing imports * change travis, dockerfile, README to use ndmg as entrypoint rather than ndmg_bids * Update cloud_utils.py * add warning to native-space registration * hotfix for dockerfile * added timer decorator * remove old comments, add new comments, clean, add stuff to setup.py * move test file, clean up setup.py * clean up a couple functions * remove some dependencies * heavily sexify setup.py * revert setup, decided the version I made was too weird * fix setup script * remove comments in setup script * fstring conversion * update pybids dependency, add checks for bids formatting * add BIDs check * More f-string * so many f-strings * goodbye %s strings * fix naming error * start to fix up sweep_directory * add DirectorySweeper class * update ndmg_bids for DirectorySweeper * comment sweep_directory out, since depracated * fix minor bugs * add pathlib to gen_utils * we already have an function in gen_utils, just called that * add json importing * continuously improving log output * add docstrings to DirectorySweeper * delete commented out sweep_directory, fix some typos * ensure that dependencies are up to date in setup.py * fix pybids version in Dockerfile * OS check, atlas change, and timer decorator placement * renovate ndmg_bids * add welcome message to ndmg_dwi_pipeline * better commenting on parcellation code * rename properly * delete session_level function * fix bug in DirectorySweeper * forgot to save * path error fix * return removal * finalize DirectorySweeper * fix last bugs * small changes to docstrings * boto3 update * output directory should include subject and session now * fix error message * docstring finishing touches * boto3 overhaul * Update ndmg_bids.py * Update ndmg_bids.py * Update ndmg_bids.py * implement PR edit suggestions * fixed str.strip error * timer change * readability improvements * minor code style changes * BUG: fix bug in DirectorySweeper warning statement * remove debug, clean * remove dataset flag, rename space * use triple-quotes for multiline strings * Update ndmg_bids.py wasn't printing if ndmg failed * Update gen_utils.py remove warnings * Update gen_utils.py * Update gen_utils.py move imports * renovate DirectorySweeper to not pass data through DataFrames * Final changes to DirectorySweeper * Update README.md * Update README.md * pytest input directory generation * improve error handling, refactor s3 code * remove missing clean from ndmg_dwi_pipeline * Update README.md * clean s3 logic * remove input dir in s3 if it already exists * fix bug in parse_path * move print statement * remove MNI space pipeline * black everything * Check that all files found by DirSweep exist * added additional checks * move print statement and delete %s * fix bugs pylint found * Update __init__.py * move affine code to track.py * trk_header argument to RunTrack.make_hdr * change printing for initial local variables * fix bug in GraphTools * Clean up * format black * clean up bval check, native/native_dsn logic * update push location code * PR edits * expand directory tree fixture * test ValueError fix * push location changes * fix push code * cleanup * ensurance for fewer bugs in push * change variable name * remove try/except in top-level loop * make bids assertion more clear * turn check_exists into print_arguments, changing role and function inputs * docstring updates * clean print statement, only print input checking once * fix reset * rename registration + eddy skipping, reformat eddy correct skip code * make eddy check sexy, replace eddy_correct cmd call * purge execute_cmd * purge os.system calls * make directories differently * skull defaults to None instead of none, fix subprocess imports * fix typo * fix applyxfm * fix apply_warp * fix imports * change output message in decorator * Qa tensor estimation pr (#369) * Update README.md * new changes * adding test data folder and unit test for rescale bvec * add a tutorial for windows users * changes * delete * merge * adding make_gtab_and_bmask unittest + some file organization * adding non fsl make_gtab_and_bmask * test of align function * adjust make_gtab_and_bmask readability * data of test input and output * creat a file of input data and output data * add a test file * add new data file * add lfs * add test data * tests/BNU1/sub-0025864/ses-1/anat/sub-0025864_ses-1_T1w.nii * lllll * add a lfs * another lfs * add code file * add code file * test of align_nonlinear * commit file * test inputs of test_apply_warp.py * changes * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * adding two unit tests and namer example * adding incomplete test_dmri_reg_class * lfs adding data * adding unit test guidelines * changes * add files * changes * upgrading code quality of unit tests and organizing folders appropriately * Update to execute pytest in correct folder * Making this defunct unittest pass. Will allow travis pytest to succeed * git add test_inverse_warp.py via command line * changes * changes * test_scripts changing via command line * change the test_scripts * code review segment_t1w * Revert version to neurodata (delete and copied over) fixing jialin's accidental edit and push * Update/merge test_rescale_bvec.py removed other version. merged * Revert "Kjl" * change the test_applyxfm * add segment_t1w * change name * Update Unit_Test_Guidelines.md markdown titles * Update Unit_Test_Guidelines.md new lines on imports * Update Unit_Test_Guidelines.md * Update Unit_Test_Guidelines.md * Update Unit_Test_Guidelines.md * Update Unit_Test_Guidelines.md * Pull NDD/ndmg instead of neurodata/ndmg * changes * Update travis.yml * blank commit to test travis * fixing some unit tests * fixing unit tests errors * Revert "Fix unit test imports for travis" * adding other merge files * clean copying from neurodata/ndmg staging * adding missing files * initial tensor qa notebook * updated tensor qa visualization * updated tensor vis * update travis with our repo keys * updated travis * travis key 3 * new travis code & merged in staging_tmp from neurodata * reinstating Dockerfile * fixing space in Dockerfile * updated track,qa,pipeline * stashing current qa commits * new travis code * travis round 100000 * updated * travis round 99999999999 * more travis * travis with aws codes that work * final qa_tensory figure * PR commit with tutorial * updated pipeline * Update .travis.yml I'm commenting out your guys's aws travis stuff for now, and we'll re-add it later once things are merged in. * Update .travis.yml one more comment for print statement * Remove old tutorial notebook * adding qa_utils, updated qa_tensor with docstrings and pr requested changes, slightly updated notebook to accompany changes * updated docstrings for qa_tensor and qa_utils * adding another functional arguments for pad_im * remove useless slices docstring * New qa fast pr (#370) * Update README.md * new changes * adding test data folder and unit test for rescale bvec * add a tutorial for windows users * changes * delete * merge * adding make_gtab_and_bmask unittest + some file organization * adding non fsl make_gtab_and_bmask * test of align function * adjust make_gtab_and_bmask readability * data of test input and output * creat a file of input data and output data * add a test file * add new data file * add lfs * add test data * tests/BNU1/sub-0025864/ses-1/anat/sub-0025864_ses-1_T1w.nii * lllll * add a lfs * another lfs * add code file * add code file * test of align_nonlinear * commit file * test inputs of test_apply_warp.py * changes * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * adding two unit tests and namer example * adding incomplete test_dmri_reg_class * lfs adding data * adding unit test guidelines * changes * add files * changes * upgrading code quality of unit tests and organizing folders appropriately * Update to execute pytest in correct folder * Making this defunct unittest pass. Will allow travis pytest to succeed * git add test_inverse_warp.py via command line * changes * changes * test_scripts changing via command line * change the test_scripts * code review segment_t1w * Revert version to neurodata (delete and copied over) fixing jialin's accidental edit and push * Update/merge test_rescale_bvec.py removed other version. merged * Revert "Kjl" * change the test_applyxfm * add segment_t1w * change name * Update Unit_Test_Guidelines.md markdown titles * Update Unit_Test_Guidelines.md new lines on imports * Update Unit_Test_Guidelines.md * Update Unit_Test_Guidelines.md * Update Unit_Test_Guidelines.md * Update Unit_Test_Guidelines.md * Pull NDD/ndmg instead of neurodata/ndmg * changes * Update travis.yml * blank commit to test travis * fixing some unit tests * fixing unit tests errors * Revert "Fix unit test imports for travis" * adding other merge files * clean copying from neurodata/ndmg staging * adding missing files * update travis with our repo keys * updated travis * travis key 3 * new travis code & merged in staging_tmp from neurodata * new_qa_fast_pr * modify * Dockerfile changes * reinstating Dockerfile * fixing space in Dockerfile * pip install tkinter in requirements.txt * travis add pip install -r requirements * add pythotk into requirements.txt * add two pip install command * apt get install python3-tk * add Y * add run command * original * delete mal * changes trives * add files * dvsdc * new travis code * travis round 100000 * travis round 99999999999 * more travis * travis with aws codes that work * wdcbsb * add np.padding * modify travis * ewso * new tutorial * shandbcbc * all changes in * all changes in * all changes in * last commit changes all in * jupyter changes * changes * changes * qa util * all changes in * the last change * the last change * new tutorial * the changes od output_dir * delete tutorial * tutorial change * tutorial change * change if arise * a few changes of qa_fast and qa_fast tutorial * chenges of pad * change of qa fast tutorial * empty line add * add wilson pr code * the last commit * the last commit of nifti * run tutorial of qa fast * LAST * LAST * LAST * changes of tutorial * changes of tutorial * wilson tutorial * code cell * changes * changes * Qa tractography pr (#375) * Update README.md * new changes * adding test data folder and unit test for rescale bvec * add a tutorial for windows users * changes * delete * merge * adding make_gtab_and_bmask unittest + some file organization * adding non fsl make_gtab_and_bmask * test of align function * adjust make_gtab_and_bmask readability * data of test input and output * creat a file of input data and output data * add a test file * add new data file * add lfs * add test data * tests/BNU1/sub-0025864/ses-1/anat/sub-0025864_ses-1_T1w.nii * lllll * add a lfs * another lfs * add code file * add code file * test of align_nonlinear * commit file * test inputs of test_apply_warp.py * changes * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * adding two unit tests and namer example * adding incomplete test_dmri_reg_class * lfs adding data * adding unit test guidelines * changes * add files * changes * upgrading code quality of unit tests and organizing folders appropriately * Update to execute pytest in correct folder * Making this defunct unittest pass. Will allow travis pytest to succeed * git add test_inverse_warp.py via command line * changes * changes * test_scripts changing via command line * change the test_scripts * code review segment_t1w * Revert version to neurodata (delete and copied over) fixing jialin's accidental edit and push * Update/merge test_rescale_bvec.py removed other version. merged * Revert "Kjl" * change the test_applyxfm * add segment_t1w * change name * Update Unit_Test_Guidelines.md markdown titles * Update Unit_Test_Guidelines.md new lines on imports * Update Unit_Test_Guidelines.md * Update Unit_Test_Guidelines.md * Update Unit_Test_Guidelines.md * Update Unit_Test_Guidelines.md * Pull NDD/ndmg instead of neurodata/ndmg * changes * Update travis.yml * blank commit to test travis * fixing some unit tests * fixing unit tests errors * Revert "Fix unit test imports for travis" * adding other merge files * clean copying from neurodata/ndmg staging * adding missing files * update travis with our repo keys * updated travis * travis key 3 * new travis code & merged in staging_tmp from neurodata * reinstating Dockerfile * fixing space in Dockerfile * new travis code * travis round 100000 * travis round 99999999999 * more travis * travis with aws codes that work * Update .travis.yml I'm commenting out your guys's aws travis stuff for now, and we'll re-add it later once things are merged in. * Update .travis.yml one more comment for print statement * PR qa edits * please work * Update .travis.yml * please again * close the opend Image * Change the location of the QA_tractography * change the tutorial * change the tutorial * please * changing the qa_tractography and the tutorial * Test qa registration pr (#372) * Update README.md * new changes * adding test data folder and unit test for rescale bvec * add a tutorial for windows users * changes * delete * merge * adding make_gtab_and_bmask unittest + some file organization * adding non fsl make_gtab_and_bmask * test of align function * adjust make_gtab_and_bmask readability * data of test input and output * creat a file of input data and output data * add a test file * add new data file * add lfs * add test data * tests/BNU1/sub-0025864/ses-1/anat/sub-0025864_ses-1_T1w.nii * lllll * add a lfs * another lfs * add code file * add code file * test of align_nonlinear * commit file * test inputs of test_apply_warp.py * changes * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * adding two unit tests and namer example * adding incomplete test_dmri_reg_class * lfs adding data * adding unit test guidelines * changes * add files * changes * upgrading code quality of unit tests and organizing folders appropriately * Update to execute pytest in correct folder * Making this defunct unittest pass. Will allow travis pytest to succeed * git add test_inverse_warp.py via command line * changes * changes * test_scripts changing via command line * change the test_scripts * code review segment_t1w * Revert version to neurodata (delete and copied over) fixing jialin's accidental edit and push * Update/merge test_rescale_bvec.py removed other version. merged * Revert "Kjl" * change the test_applyxfm * add segment_t1w * change name * Update Unit_Test_Guidelines.md markdown titles * Update Unit_Test_Guidelines.md new lines on imports * Update Unit_Test_Guidelines.md * Update Unit_Test_Guidelines.md * Update Unit_Test_Guidelines.md * Update Unit_Test_Guidelines.md * Pull NDD/ndmg instead of neurodata/ndmg * changes * Update travis.yml * blank commit to test travis * fixing some unit tests * fixing unit tests errors * Revert "Fix unit test imports for travis" * adding other merge files * clean copying from neurodata/ndmg staging * adding missing files * update travis with our repo keys * updated travis * travis key 3 * new travis code & merged in staging_tmp from neurodata * reinstating Dockerfile * fixing space in Dockerfile * test changes * trivial changes for dockerfile to test * new travis code * travis round 100000 * test_passed * travis round 99999999999 * more travis * travis with aws codes that work * zero pad images * trivial changes * title changes * Update .travis.yml I'm commenting out your guys's aws travis stuff for now, and we'll re-add it later once things are merged in. * Update .travis.yml one more comment for print statement * changes on docstrings * changes on fname * changes on tutorials and import * remove copyright text * change fnames * doctrings * get_filename shortened * tutorial changes * resolve conflicts * tutorial changes * tutorial changes * resolve conflicts * change on import * conflicts * Qa skullstrip pr (#366) * Update README.md * new changes * adding test data folder and unit test for rescale bvec * add a tutorial for windows users * changes * delete * merge * adding make_gtab_and_bmask unittest + some file organization * adding non fsl make_gtab_and_bmask * test of align function * adjust make_gtab_and_bmask readability * data of test input and output * creat a file of input data and output data * add a test file * add new data file * add lfs * add test data * tests/BNU1/sub-0025864/ses-1/anat/sub-0025864_ses-1_T1w.nii * lllll * add a lfs * another lfs * add code file * add code file * test of align_nonlinear * commit file * test inputs of test_apply_warp.py * changes * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * adding two unit tests and namer example * adding incomplete test_dmri_reg_class * lfs adding data * adding unit test guidelines * changes * add files * changes * upgrading code quality of unit tests and organizing folders appropriately * Update to execute pytest in correct folder * Making this defunct unittest pass. Will allow travis pytest to succeed * git add test_inverse_warp.py via command line * changes * changes * test_scripts changing via command line * change the test_scripts * code review segment_t1w * Revert version to neurodata (delete and copied over) fixing jialin's accidental edit and push * Update/merge test_rescale_bvec.py removed other version. merged * Revert "Kjl" * change the test_applyxfm * add segment_t1w * change name * Update Unit_Test_Guidelines.md markdown titles * Update Unit_Test_Guidelines.md new lines on imports * Update Unit_Test_Guidelines.md * Update Unit_Test_Guidelines.md * Update Unit_Test_Guidelines.md * Update Unit_Test_Guidelines.md * Pull NDD/ndmg instead of neurodata/ndmg * changes * Update travis.yml * blank commit to test travis * fixing some unit tests * fixing unit tests errors * Revert "Fix unit test imports for travis" * adding other merge files * clean copying from neurodata/ndmg staging * adding missing files * update travis with our repo keys * updated travis * travis key 3 * new travis code & merged in staging_tmp from neurodata * reinstating Dockerfile * fixing space in Dockerfile * add function qa skull strip * fix travis, same as ndmg_tmp * ready to pr * reverse register.py * new travis code * travis round 100000 * travis round 99999999999 * more travis * travis with aws codes that work * try if travis works, please ignore this version * fix register.py and try if travis works, please ignore this version * Update .travis.yml I'm commenting out your guys's aws travis stuff for now, and we'll re-add it later once things are merged in. * Update .travis.yml one more comment for print statement * qa_skullstrip * reverse travis * add qa_utils * fix qa_skullstrip, path problem * fix path * change jupyter notebook * change notebook * fix tutorial * fix some problems, still have some work to do * change some code, don't know if it works * fix register * change qa_utils * Delete Qa_skullstrip.ipynb * change tutorial * fix some docstring * change docstring and variables * docstring * ignore it * delete duplicated code * change docstring for gettruevolume * tutorial * tutorial,done * change word in tutorial * change word plotting * tutorial add code cell * update tutorial * update tutorial * add teammates function * up to date * fix conflict * Exorcise namer (#374) * fix __init__ * delete regex that wasnt being used, change location, remove unused functions * namer now subclasses UserDict (it is now itself a dictionary) * delete unecessary method, start refactoring self.add_dirs * BEGIN EXORCISM * delete namer entirely, fix bvec movement * fix initial directory tree creation * remove namer from gen_utils.reorient_dwi, fix loadGraphs * namer purged from max_target_vox_res (along with cleanup operations on same) * refactor skipreg code to avoid namer - not as happy with this as with skipeddy refactor, but spent less time on it * remove namer from gen_utils.reorient_t1w * purge namer from DmriReg * wrap subprocess.run so the shell prints executed commands * change name to * change log print statement * add toggle to return as path to gen_utils.as_directory * simplify reg skipping code * new checks * fix skullstrip_files and skipreg bug, add debugging to reorient_t1w * fix debugging prints, add argument unpacking to skullstrip_check * further debugging for travis * fix print statements * print nibabel version * fix print statement * print directory creation * I think this fixed the filepath bug * print parent path * fix skullstrip_check bug * remove namer from graph code * fix typo in ndmg_bids * it is done. namer has been defeated. we may rest now, and watch the sun rise on a grateful universe. * ...fix travis, fix issues I found PR review * controversial change: delete everything in stats, to be replaced by the NDD groups modules * remove namer from wilsons tensor qa * extra parenthesis * remove s3 stuff until NDD people finish PRs * add travis s3 back in * fix syntax error, fix bug in s3 pulling code * fix another syntax error * account for name rename * fix s3 pushing * unclear why travis thinks connectome output directory doesn't exist, adding some checks * closing parenthesis on print statement * maybe the last commit * update the way variable checks for slashes * rename to m2g * fix docker typo * fixed renaming typo * change qa_tractography docker if statement * changed branch being pulled from in docker file * fix _init_ merge conflict * added warnings import * update aws templates to m2g * travis updates * update job_definition * changed job definition * Update README.md * Add contributing file (#387) * Create CONTRIBUTING.md * Update CONTRIBUTING.md * Update CONTRIBUTING.md * Update CONTRIBUTING.md * Update CONTRIBUTING.md * Update CONTRIBUTING.md we'll change this back to "master" once we've changed the name and deleted old master * Update CONTRIBUTING.md typo * Update CONTRIBUTING.md there is about 1% variation from noise in discriminability, as far as we can tell, so added that clause to improvement criteria * Update CONTRIBUTING.md * Update CONTRIBUTING.md add clause for merge conflicts * Update CONTRIBUTING.md * Update CONTRIBUTING.md Co-authored-by: Alex Loftus <alexloftus2004@gmail.com> * Update CONTRIBUTING.md * change ndmg to m2g Co-authored-by: Alex Loftus <alexloftus2004@gmail.com> Co-authored-by: wilttang <wilsontimtang@gmail.com> Co-authored-by: JialinKang <54913794+JialinKang@users.noreply.github.com> Co-authored-by: Zhen Hu <huzhen_shtech@163.com> Co-authored-by: FangCai <54511589+FangCai-fifi@users.noreply.github.com> Co-authored-by: Chuankai_Luo <55203069+luochuankai-JHU@users.noreply.github.com>
Lawreros
added a commit
that referenced
this pull request
Feb 12, 2020
* write dope decorator, add it to everything in reg_utils * fixed issue with import changes * Revert "write dope decorator, add it to everything in reg_utils" This reverts commit a3b8047. * fixed misnamed function * gen_reg change test * fix * Added skull parameter * fixed stupid mistake * Update ndmg_bids.py * Update gen_reg.py * Update reg_utils.py * added key-error function * added file renaming * test * test * test * add comands run inside docker container * test * added missing "done" * docker copy * directory update * directory update * Update reg_utils.py * aws testrun key encryption aws key update test s3 change branch addition test str change one last shot New approach fix docker error fix typos re-encryption test encrypt_test s3 fix push connectome data Added branch and commit information reorganize Fold check Formatting check switch back travis fix line deletion echo deletion * travis_fold test * foldv2 * html addition * Dipy newversion (#311) * initial dependency fix * fix up dipy imports in gen_track * organize imports in gen_track * rename all classifiers, add some TODOs * many renames * iterrated through everything but EudXDirectionGetter * fix gen_graph error * fix dsn * fix bug in dsn * native_dsn is totally fixed now * add clearer print statements * write dope decorator, add to a bunch of functions in gen_utils * fix merge conflict * fiddling with check_exists arguments a bit * functions get displayed with check_exists, so removing print statements * remove mni space for now. Fix before merge into deploy. * clearer decorator * remove some old func code * remove mni from travis * remove comment * fix graph saving * no check_exists on skullstrip_check * check for TypeError in check_exists * format fix * Remove non-html * Removed git lfs neuroparc * black on all files * change mgu to gen_utils * simplify get_filename, delete extra function * remove fmri func * remove extract_mask * remove bet skullstrip function * remove reslice_to_xmm, not used * remove get_sphere, as we use the dipy func instead * remove function from name_resource, change mgu naming conventions * remove unecessary methods from gen_graph * remove get_status from ndmg_cloud, unecessary function * organize imports across ndmg * black on all files (#319) * Update Dockerfile * Update .travis.yml * change class naming syntax for all classes * rename more classes, change module name * s3_utils to cloud_utils everywhere * Revert "Travis deploy" * BREAK THE WORLD AND PURGE EVERYTHING, CHAOTIC GOOD, ENTIRE MODULE ORGANIZATION CHANGED * Push travis output to s3 bucket * remove script that wasnt doing anything * merge conflict in setup.py * fix merge conflicts * the world is currently on fire, but will soon be reborn anew, like a phoenix * ndmg now pip installs again * add functools.wraps to check_exists, add ndmg_bids as a backwards-compatibilty option to setup.py * add proper imports * some missing imports in dwi_pipeline * finish organizing imports * change travis, dockerfile, README to use ndmg as entrypoint rather than ndmg_bids * Update cloud_utils.py * add warning to native-space registration * hotfix for dockerfile * added timer decorator * remove old comments, add new comments, clean, add stuff to setup.py * move test file, clean up setup.py * clean up a couple functions * remove some dependencies * heavily sexify setup.py * revert setup, decided the version I made was too weird * fix setup script * remove comments in setup script * fstring conversion * update pybids dependency, add checks for bids formatting * add BIDs check * More f-string * so many f-strings * goodbye %s strings * fix naming error * start to fix up sweep_directory * add DirectorySweeper class * update ndmg_bids for DirectorySweeper * comment sweep_directory out, since depracated * fix minor bugs * add pathlib to gen_utils * we already have an function in gen_utils, just called that * add json importing * continuously improving log output * add docstrings to DirectorySweeper * delete commented out sweep_directory, fix some typos * ensure that dependencies are up to date in setup.py * fix pybids version in Dockerfile * OS check, atlas change, and timer decorator placement * renovate ndmg_bids * add welcome message to ndmg_dwi_pipeline * better commenting on parcellation code * rename properly * delete session_level function * fix bug in DirectorySweeper * forgot to save * path error fix * return removal * finalize DirectorySweeper * fix last bugs * small changes to docstrings * boto3 update * output directory should include subject and session now * fix error message * docstring finishing touches * boto3 overhaul * Update ndmg_bids.py * Update ndmg_bids.py * Update ndmg_bids.py * implement PR edit suggestions * fixed str.strip error * timer change * readability improvements * minor code style changes * BUG: fix bug in DirectorySweeper warning statement * remove debug, clean * remove dataset flag, rename space * use triple-quotes for multiline strings * Update ndmg_bids.py wasn't printing if ndmg failed * Update gen_utils.py remove warnings * Update gen_utils.py * Update gen_utils.py move imports * renovate DirectorySweeper to not pass data through DataFrames * Final changes to DirectorySweeper * Update README.md * Update README.md * pytest input directory generation * improve error handling, refactor s3 code * remove missing clean from ndmg_dwi_pipeline * Update README.md * clean s3 logic * remove input dir in s3 if it already exists * fix bug in parse_path * move print statement * remove MNI space pipeline * black everything * Check that all files found by DirSweep exist * added additional checks * move print statement and delete %s * fix bugs pylint found * Update __init__.py * move affine code to track.py * trk_header argument to RunTrack.make_hdr * change printing for initial local variables * fix bug in GraphTools * Clean up * format black * clean up bval check, native/native_dsn logic * update push location code * PR edits * expand directory tree fixture * test ValueError fix * push location changes * fix push code * cleanup * ensurance for fewer bugs in push * change variable name * remove try/except in top-level loop * make bids assertion more clear * turn check_exists into print_arguments, changing role and function inputs * docstring updates * clean print statement, only print input checking once * fix reset * rename registration + eddy skipping, reformat eddy correct skip code * make eddy check sexy, replace eddy_correct cmd call * purge execute_cmd * purge os.system calls * make directories differently * skull defaults to None instead of none, fix subprocess imports * fix typo * fix applyxfm * fix apply_warp * fix imports * change output message in decorator * Qa tensor estimation pr (#369) * Update README.md * new changes * adding test data folder and unit test for rescale bvec * add a tutorial for windows users * changes * delete * merge * adding make_gtab_and_bmask unittest + some file organization * adding non fsl make_gtab_and_bmask * test of align function * adjust make_gtab_and_bmask readability * data of test input and output * creat a file of input data and output data * add a test file * add new data file * add lfs * add test data * tests/BNU1/sub-0025864/ses-1/anat/sub-0025864_ses-1_T1w.nii * lllll * add a lfs * another lfs * add code file * add code file * test of align_nonlinear * commit file * test inputs of test_apply_warp.py * changes * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * adding two unit tests and namer example * adding incomplete test_dmri_reg_class * lfs adding data * adding unit test guidelines * changes * add files * changes * upgrading code quality of unit tests and organizing folders appropriately * Update to execute pytest in correct folder * Making this defunct unittest pass. Will allow travis pytest to succeed * git add test_inverse_warp.py via command line * changes * changes * test_scripts changing via command line * change the test_scripts * code review segment_t1w * Revert version to neurodata (delete and copied over) fixing jialin's accidental edit and push * Update/merge test_rescale_bvec.py removed other version. merged * Revert "Kjl" * change the test_applyxfm * add segment_t1w * change name * Update Unit_Test_Guidelines.md markdown titles * Update Unit_Test_Guidelines.md new lines on imports * Update Unit_Test_Guidelines.md * Update Unit_Test_Guidelines.md * Update Unit_Test_Guidelines.md * Update Unit_Test_Guidelines.md * Pull NDD/ndmg instead of neurodata/ndmg * changes * Update travis.yml * blank commit to test travis * fixing some unit tests * fixing unit tests errors * Revert "Fix unit test imports for travis" * adding other merge files * clean copying from neurodata/ndmg staging * adding missing files * initial tensor qa notebook * updated tensor qa visualization * updated tensor vis * update travis with our repo keys * updated travis * travis key 3 * new travis code & merged in staging_tmp from neurodata * reinstating Dockerfile * fixing space in Dockerfile * updated track,qa,pipeline * stashing current qa commits * new travis code * travis round 100000 * updated * travis round 99999999999 * more travis * travis with aws codes that work * final qa_tensory figure * PR commit with tutorial * updated pipeline * Update .travis.yml I'm commenting out your guys's aws travis stuff for now, and we'll re-add it later once things are merged in. * Update .travis.yml one more comment for print statement * Remove old tutorial notebook * adding qa_utils, updated qa_tensor with docstrings and pr requested changes, slightly updated notebook to accompany changes * updated docstrings for qa_tensor and qa_utils * adding another functional arguments for pad_im * remove useless slices docstring * New qa fast pr (#370) * Update README.md * new changes * adding test data folder and unit test for rescale bvec * add a tutorial for windows users * changes * delete * merge * adding make_gtab_and_bmask unittest + some file organization * adding non fsl make_gtab_and_bmask * test of align function * adjust make_gtab_and_bmask readability * data of test input and output * creat a file of input data and output data * add a test file * add new data file * add lfs * add test data * tests/BNU1/sub-0025864/ses-1/anat/sub-0025864_ses-1_T1w.nii * lllll * add a lfs * another lfs * add code file * add code file * test of align_nonlinear * commit file * test inputs of test_apply_warp.py * changes * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * adding two unit tests and namer example * adding incomplete test_dmri_reg_class * lfs adding data * adding unit test guidelines * changes * add files * changes * upgrading code quality of unit tests and organizing folders appropriately * Update to execute pytest in correct folder * Making this defunct unittest pass. Will allow travis pytest to succeed * git add test_inverse_warp.py via command line * changes * changes * test_scripts changing via command line * change the test_scripts * code review segment_t1w * Revert version to neurodata (delete and copied over) fixing jialin's accidental edit and push * Update/merge test_rescale_bvec.py removed other version. merged * Revert "Kjl" * change the test_applyxfm * add segment_t1w * change name * Update Unit_Test_Guidelines.md markdown titles * Update Unit_Test_Guidelines.md new lines on imports * Update Unit_Test_Guidelines.md * Update Unit_Test_Guidelines.md * Update Unit_Test_Guidelines.md * Update Unit_Test_Guidelines.md * Pull NDD/ndmg instead of neurodata/ndmg * changes * Update travis.yml * blank commit to test travis * fixing some unit tests * fixing unit tests errors * Revert "Fix unit test imports for travis" * adding other merge files * clean copying from neurodata/ndmg staging * adding missing files * update travis with our repo keys * updated travis * travis key 3 * new travis code & merged in staging_tmp from neurodata * new_qa_fast_pr * modify * Dockerfile changes * reinstating Dockerfile * fixing space in Dockerfile * pip install tkinter in requirements.txt * travis add pip install -r requirements * add pythotk into requirements.txt * add two pip install command * apt get install python3-tk * add Y * add run command * original * delete mal * changes trives * add files * dvsdc * new travis code * travis round 100000 * travis round 99999999999 * more travis * travis with aws codes that work * wdcbsb * add np.padding * modify travis * ewso * new tutorial * shandbcbc * all changes in * all changes in * all changes in * last commit changes all in * jupyter changes * changes * changes * qa util * all changes in * the last change * the last change * new tutorial * the changes od output_dir * delete tutorial * tutorial change * tutorial change * change if arise * a few changes of qa_fast and qa_fast tutorial * chenges of pad * change of qa fast tutorial * empty line add * add wilson pr code * the last commit * the last commit of nifti * run tutorial of qa fast * LAST * LAST * LAST * changes of tutorial * changes of tutorial * wilson tutorial * code cell * changes * changes * Qa tractography pr (#375) * Update README.md * new changes * adding test data folder and unit test for rescale bvec * add a tutorial for windows users * changes * delete * merge * adding make_gtab_and_bmask unittest + some file organization * adding non fsl make_gtab_and_bmask * test of align function * adjust make_gtab_and_bmask readability * data of test input and output * creat a file of input data and output data * add a test file * add new data file * add lfs * add test data * tests/BNU1/sub-0025864/ses-1/anat/sub-0025864_ses-1_T1w.nii * lllll * add a lfs * another lfs * add code file * add code file * test of align_nonlinear * commit file * test inputs of test_apply_warp.py * changes * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * adding two unit tests and namer example * adding incomplete test_dmri_reg_class * lfs adding data * adding unit test guidelines * changes * add files * changes * upgrading code quality of unit tests and organizing folders appropriately * Update to execute pytest in correct folder * Making this defunct unittest pass. Will allow travis pytest to succeed * git add test_inverse_warp.py via command line * changes * changes * test_scripts changing via command line * change the test_scripts * code review segment_t1w * Revert version to neurodata (delete and copied over) fixing jialin's accidental edit and push * Update/merge test_rescale_bvec.py removed other version. merged * Revert "Kjl" * change the test_applyxfm * add segment_t1w * change name * Update Unit_Test_Guidelines.md markdown titles * Update Unit_Test_Guidelines.md new lines on imports * Update Unit_Test_Guidelines.md * Update Unit_Test_Guidelines.md * Update Unit_Test_Guidelines.md * Update Unit_Test_Guidelines.md * Pull NDD/ndmg instead of neurodata/ndmg * changes * Update travis.yml * blank commit to test travis * fixing some unit tests * fixing unit tests errors * Revert "Fix unit test imports for travis" * adding other merge files * clean copying from neurodata/ndmg staging * adding missing files * update travis with our repo keys * updated travis * travis key 3 * new travis code & merged in staging_tmp from neurodata * reinstating Dockerfile * fixing space in Dockerfile * new travis code * travis round 100000 * travis round 99999999999 * more travis * travis with aws codes that work * Update .travis.yml I'm commenting out your guys's aws travis stuff for now, and we'll re-add it later once things are merged in. * Update .travis.yml one more comment for print statement * PR qa edits * please work * Update .travis.yml * please again * close the opend Image * Change the location of the QA_tractography * change the tutorial * change the tutorial * please * changing the qa_tractography and the tutorial * Test qa registration pr (#372) * Update README.md * new changes * adding test data folder and unit test for rescale bvec * add a tutorial for windows users * changes * delete * merge * adding make_gtab_and_bmask unittest + some file organization * adding non fsl make_gtab_and_bmask * test of align function * adjust make_gtab_and_bmask readability * data of test input and output * creat a file of input data and output data * add a test file * add new data file * add lfs * add test data * tests/BNU1/sub-0025864/ses-1/anat/sub-0025864_ses-1_T1w.nii * lllll * add a lfs * another lfs * add code file * add code file * test of align_nonlinear * commit file * test inputs of test_apply_warp.py * changes * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * adding two unit tests and namer example * adding incomplete test_dmri_reg_class * lfs adding data * adding unit test guidelines * changes * add files * changes * upgrading code quality of unit tests and organizing folders appropriately * Update to execute pytest in correct folder * Making this defunct unittest pass. Will allow travis pytest to succeed * git add test_inverse_warp.py via command line * changes * changes * test_scripts changing via command line * change the test_scripts * code review segment_t1w * Revert version to neurodata (delete and copied over) fixing jialin's accidental edit and push * Update/merge test_rescale_bvec.py removed other version. merged * Revert "Kjl" * change the test_applyxfm * add segment_t1w * change name * Update Unit_Test_Guidelines.md markdown titles * Update Unit_Test_Guidelines.md new lines on imports * Update Unit_Test_Guidelines.md * Update Unit_Test_Guidelines.md * Update Unit_Test_Guidelines.md * Update Unit_Test_Guidelines.md * Pull NDD/ndmg instead of neurodata/ndmg * changes * Update travis.yml * blank commit to test travis * fixing some unit tests * fixing unit tests errors * Revert "Fix unit test imports for travis" * adding other merge files * clean copying from neurodata/ndmg staging * adding missing files * update travis with our repo keys * updated travis * travis key 3 * new travis code & merged in staging_tmp from neurodata * reinstating Dockerfile * fixing space in Dockerfile * test changes * trivial changes for dockerfile to test * new travis code * travis round 100000 * test_passed * travis round 99999999999 * more travis * travis with aws codes that work * zero pad images * trivial changes * title changes * Update .travis.yml I'm commenting out your guys's aws travis stuff for now, and we'll re-add it later once things are merged in. * Update .travis.yml one more comment for print statement * changes on docstrings * changes on fname * changes on tutorials and import * remove copyright text * change fnames * doctrings * get_filename shortened * tutorial changes * resolve conflicts * tutorial changes * tutorial changes * resolve conflicts * change on import * conflicts * Qa skullstrip pr (#366) * Update README.md * new changes * adding test data folder and unit test for rescale bvec * add a tutorial for windows users * changes * delete * merge * adding make_gtab_and_bmask unittest + some file organization * adding non fsl make_gtab_and_bmask * test of align function * adjust make_gtab_and_bmask readability * data of test input and output * creat a file of input data and output data * add a test file * add new data file * add lfs * add test data * tests/BNU1/sub-0025864/ses-1/anat/sub-0025864_ses-1_T1w.nii * lllll * add a lfs * another lfs * add code file * add code file * test of align_nonlinear * commit file * test inputs of test_apply_warp.py * changes * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * adding two unit tests and namer example * adding incomplete test_dmri_reg_class * lfs adding data * adding unit test guidelines * changes * add files * changes * upgrading code quality of unit tests and organizing folders appropriately * Update to execute pytest in correct folder * Making this defunct unittest pass. Will allow travis pytest to succeed * git add test_inverse_warp.py via command line * changes * changes * test_scripts changing via command line * change the test_scripts * code review segment_t1w * Revert version to neurodata (delete and copied over) fixing jialin's accidental edit and push * Update/merge test_rescale_bvec.py removed other version. merged * Revert "Kjl" * change the test_applyxfm * add segment_t1w * change name * Update Unit_Test_Guidelines.md markdown titles * Update Unit_Test_Guidelines.md new lines on imports * Update Unit_Test_Guidelines.md * Update Unit_Test_Guidelines.md * Update Unit_Test_Guidelines.md * Update Unit_Test_Guidelines.md * Pull NDD/ndmg instead of neurodata/ndmg * changes * Update travis.yml * blank commit to test travis * fixing some unit tests * fixing unit tests errors * Revert "Fix unit test imports for travis" * adding other merge files * clean copying from neurodata/ndmg staging * adding missing files * update travis with our repo keys * updated travis * travis key 3 * new travis code & merged in staging_tmp from neurodata * reinstating Dockerfile * fixing space in Dockerfile * add function qa skull strip * fix travis, same as ndmg_tmp * ready to pr * reverse register.py * new travis code * travis round 100000 * travis round 99999999999 * more travis * travis with aws codes that work * try if travis works, please ignore this version * fix register.py and try if travis works, please ignore this version * Update .travis.yml I'm commenting out your guys's aws travis stuff for now, and we'll re-add it later once things are merged in. * Update .travis.yml one more comment for print statement * qa_skullstrip * reverse travis * add qa_utils * fix qa_skullstrip, path problem * fix path * change jupyter notebook * change notebook * fix tutorial * fix some problems, still have some work to do * change some code, don't know if it works * fix register * change qa_utils * Delete Qa_skullstrip.ipynb * change tutorial * fix some docstring * change docstring and variables * docstring * ignore it * delete duplicated code * change docstring for gettruevolume * tutorial * tutorial,done * change word in tutorial * change word plotting * tutorial add code cell * update tutorial * update tutorial * add teammates function * up to date * fix conflict * Exorcise namer (#374) * fix __init__ * delete regex that wasnt being used, change location, remove unused functions * namer now subclasses UserDict (it is now itself a dictionary) * delete unecessary method, start refactoring self.add_dirs * BEGIN EXORCISM * delete namer entirely, fix bvec movement * fix initial directory tree creation * remove namer from gen_utils.reorient_dwi, fix loadGraphs * namer purged from max_target_vox_res (along with cleanup operations on same) * refactor skipreg code to avoid namer - not as happy with this as with skipeddy refactor, but spent less time on it * remove namer from gen_utils.reorient_t1w * purge namer from DmriReg * wrap subprocess.run so the shell prints executed commands * change name to * change log print statement * add toggle to return as path to gen_utils.as_directory * simplify reg skipping code * new checks * fix skullstrip_files and skipreg bug, add debugging to reorient_t1w * fix debugging prints, add argument unpacking to skullstrip_check * further debugging for travis * fix print statements * print nibabel version * fix print statement * print directory creation * I think this fixed the filepath bug * print parent path * fix skullstrip_check bug * remove namer from graph code * fix typo in ndmg_bids * it is done. namer has been defeated. we may rest now, and watch the sun rise on a grateful universe. * ...fix travis, fix issues I found PR review * controversial change: delete everything in stats, to be replaced by the NDD groups modules * remove namer from wilsons tensor qa * extra parenthesis * remove s3 stuff until NDD people finish PRs * add travis s3 back in * fix syntax error, fix bug in s3 pulling code * fix another syntax error * account for name rename * fix s3 pushing * unclear why travis thinks connectome output directory doesn't exist, adding some checks * closing parenthesis on print statement * maybe the last commit * update the way variable checks for slashes * rename to m2g * fix docker typo * fixed renaming typo * change qa_tractography docker if statement * changed branch being pulled from in docker file * fix _init_ merge conflict * added warnings import * update aws templates to m2g * travis updates * update job_definition * changed job definition * Update README.md * Add contributing file (#387) * Create CONTRIBUTING.md * Update CONTRIBUTING.md * Update CONTRIBUTING.md * Update CONTRIBUTING.md * Update CONTRIBUTING.md * Update CONTRIBUTING.md we'll change this back to "master" once we've changed the name and deleted old master * Update CONTRIBUTING.md typo * Update CONTRIBUTING.md there is about 1% variation from noise in discriminability, as far as we can tell, so added that clause to improvement criteria * Update CONTRIBUTING.md * Update CONTRIBUTING.md add clause for merge conflicts * Update CONTRIBUTING.md * Update CONTRIBUTING.md Co-authored-by: Alex Loftus <alexloftus2004@gmail.com> * Update CONTRIBUTING.md * change ndmg to m2g * remove tract option from mod_func Co-authored-by: Alex Loftus <alexloftus2004@gmail.com> Co-authored-by: wilttang <wilsontimtang@gmail.com> Co-authored-by: JialinKang <54913794+JialinKang@users.noreply.github.com> Co-authored-by: Zhen Hu <huzhen_shtech@163.com> Co-authored-by: FangCai <54511589+FangCai-fifi@users.noreply.github.com> Co-authored-by: Chuankai_Luo <55203069+luochuankai-JHU@users.noreply.github.com>
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