diff --git a/README.md b/README.md index 7dbe08a..d000d19 100644 --- a/README.md +++ b/README.md @@ -1,16 +1,34 @@ # func_processing -Pipeline used to take functional data from DICOMs through group-level analyses. Organization is as follows: +Pipeline used to take functional data from DICOMs through group-level analyses. -- cli: **User-level entrypoint.** Contains scripts to start AFNI, ASHS, fMRIprep, FreeSurfer, refacing, and data checking workflows. -- cron: Outdated. Automate cli. Can be used to schedule/automate cli usage. -- dockerfiles: Contains Dockerfile and scripts used for generating, running docker. -- docs: Resources for formal documentation, via sphinx. Instructions in build_docs.txt. -- logs: Mainly for completed_preprocessing.tsv, other output logs written here. -- qc: Files/scripts for conducting qc on pipeline workflows for non-default options. Also serves as example of user-specified timing files. -- resources: Location of modules for AFNI, ASHS, FreeSurfer, fMRIprep, and reports. -- tests: Scripts for testing resources and workflows. -- workflow: Manages resources, controlled by cli. +## Entry Points +Following `python setup.py install` or `python setup.py develop`, use the following entry points to trigger cli. -See [Wiki](https://github.com/emu-project/func_processing/wiki) for details and description. +- `check` : print help, run `cli.checks`, used to determine which participants have which preprocessed files. +- `ashs` : trigger help of `cli.ashs`, for running Automated Hippocampal Subfield Segmentation. +- `reface` : trigger help of `cli.reface`, for de/refacing participant T1w files. +- `fmriprep` : trigger help of `cli.fmriprep`, for moving data found in `dset` through FreeSurfer and fMRIPrep. +- `task_subj` : trigger help of `cli.afni_task_subj`, move task EPI output of `fmriprep` through extra preprocessing, deconvolution. +- `rs_subj` : trigger help of `cli.afni_resting_subj`, move resting EPI output of `fmriprep` through extra preprocessing, deconvolution. +- `task_group` : trigger help of `cli.afni_task_group`, conduct group-level task EPI analyses. +- `rs_group` : trigger help of `cli.afni_resting_group`, conduct group-level resting EPI analyses. -Module documentation [here](https://emu-func-processing.readthedocs.io/en/latest/), assuming sphinx is cooperative. +## Project organization + +Top Level + +- dockerfiles : Dockerfile, shell script backup +- docs : Project documentation, for [ReadTheDocs](https://emu-func-processing.readthedocs.io/en/latest/), assuming sphinx is cooperative. Build instruction found in build_docs.txt. +- func_processing : Main package + +func_processing + +- cli : Contains scripts to start AFNI, ASHS, fMRIprep, FreeSurfer, refacing, and data checking workflows. +- examples : Contains example scripts and files. +- logs : Mainly for completed_preprocessing.tsv, other output logs written here. +- resources : Location of modules for AFNI, ASHS, FreeSurfer, fMRIprep, and reports. +- tests : Scripts for testing resources and workflows. +- tools : Location for auxiliary/shell scripts. 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When it is not found, a full rebuild will be done. -config: f9ae069b753a0cb0f4029da6874faed6 +config: a4df39dc9917fefea032fc7212f5a7be tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/_build/html/_sources/func_processing.resources.afni.rst.txt b/docs/_build/html/_sources/func_processing.resources.afni.rst.txt new file mode 100644 index 0000000..a7189fd --- /dev/null +++ b/docs/_build/html/_sources/func_processing.resources.afni.rst.txt @@ -0,0 +1,69 @@ +func\_processing.resources.afni package +======================================= + +Submodules +---------- + +func\_processing.resources.afni.copy module +------------------------------------------- + +.. automodule:: func_processing.resources.afni.copy + :members: + :undoc-members: + :show-inheritance: + +func\_processing.resources.afni.deconvolve module +------------------------------------------------- + +.. automodule:: func_processing.resources.afni.deconvolve + :members: + :undoc-members: + :show-inheritance: + +func\_processing.resources.afni.group module +-------------------------------------------- + +.. automodule:: func_processing.resources.afni.group + :members: + :undoc-members: + :show-inheritance: + +func\_processing.resources.afni.masks module +-------------------------------------------- + +.. automodule:: func_processing.resources.afni.masks + :members: + :undoc-members: + :show-inheritance: + +func\_processing.resources.afni.motion module +--------------------------------------------- + +.. automodule:: func_processing.resources.afni.motion + :members: + :undoc-members: + :show-inheritance: + +func\_processing.resources.afni.process module +---------------------------------------------- + +.. automodule:: func_processing.resources.afni.process + :members: + :undoc-members: + :show-inheritance: + +func\_processing.resources.afni.submit module +--------------------------------------------- + +.. automodule:: func_processing.resources.afni.submit + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: func_processing.resources.afni + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/_build/html/_sources/func_processing.resources.ashs.rst.txt b/docs/_build/html/_sources/func_processing.resources.ashs.rst.txt new file mode 100644 index 0000000..17558c8 --- /dev/null +++ b/docs/_build/html/_sources/func_processing.resources.ashs.rst.txt @@ -0,0 +1,21 @@ +func\_processing.resources.ashs package +======================================= + +Submodules +---------- + +func\_processing.resources.ashs.hipseg module +--------------------------------------------- + +.. automodule:: func_processing.resources.ashs.hipseg + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: func_processing.resources.ashs + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/_build/html/_sources/func_processing.resources.fmriprep.rst.txt b/docs/_build/html/_sources/func_processing.resources.fmriprep.rst.txt new file mode 100644 index 0000000..bfd119c --- /dev/null +++ b/docs/_build/html/_sources/func_processing.resources.fmriprep.rst.txt @@ -0,0 +1,21 @@ +func\_processing.resources.fmriprep package +=========================================== + +Submodules +---------- + +func\_processing.resources.fmriprep.preprocess module +----------------------------------------------------- + +.. automodule:: func_processing.resources.fmriprep.preprocess + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: func_processing.resources.fmriprep + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/_build/html/_sources/func_processing.resources.reports.rst.txt b/docs/_build/html/_sources/func_processing.resources.reports.rst.txt new file mode 100644 index 0000000..c96a70d --- /dev/null +++ b/docs/_build/html/_sources/func_processing.resources.reports.rst.txt @@ -0,0 +1,21 @@ +func\_processing.resources.reports package +========================================== + +Submodules +---------- + +func\_processing.resources.reports.check\_complete module +--------------------------------------------------------- + +.. automodule:: func_processing.resources.reports.check_complete + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: func_processing.resources.reports + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/_build/html/_sources/func_processing.resources.rst.txt b/docs/_build/html/_sources/func_processing.resources.rst.txt new file mode 100644 index 0000000..d966e48 --- /dev/null +++ b/docs/_build/html/_sources/func_processing.resources.rst.txt @@ -0,0 +1,21 @@ +func\_processing.resources package +================================== + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + func_processing.resources.afni + func_processing.resources.ashs + func_processing.resources.fmriprep + func_processing.resources.reports + +Module contents +--------------- + +.. automodule:: func_processing.resources + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/resources.rst b/docs/_build/html/_sources/func_processing.rst.txt similarity index 50% rename from docs/resources.rst rename to docs/_build/html/_sources/func_processing.rst.txt index ebe59a3..ae7bd62 100644 --- a/docs/resources.rst +++ b/docs/_build/html/_sources/func_processing.rst.txt @@ -1,5 +1,5 @@ -resources package -================= +func\_processing package +======================== Subpackages ----------- @@ -7,15 +7,13 @@ Subpackages .. toctree:: :maxdepth: 4 - resources.afni - resources.ashs - resources.fmriprep - resources.reports + func_processing.resources + func_processing.workflow Module contents --------------- -.. automodule:: resources +.. automodule:: func_processing :members: :undoc-members: :show-inheritance: diff --git a/docs/_build/html/_sources/func_processing.workflow.rst.txt b/docs/_build/html/_sources/func_processing.workflow.rst.txt new file mode 100644 index 0000000..5ec1d8b --- /dev/null +++ b/docs/_build/html/_sources/func_processing.workflow.rst.txt @@ -0,0 +1,45 @@ +func\_processing.workflow package +================================= + +Submodules +---------- + +func\_processing.workflow.control\_afni module +---------------------------------------------- + +.. automodule:: func_processing.workflow.control_afni + :members: + :undoc-members: + :show-inheritance: + +func\_processing.workflow.control\_ashs module +---------------------------------------------- + +.. automodule:: func_processing.workflow.control_ashs + :members: + :undoc-members: + :show-inheritance: + +func\_processing.workflow.control\_fmriprep module +-------------------------------------------------- + +.. automodule:: func_processing.workflow.control_fmriprep + :members: + :undoc-members: + :show-inheritance: + +func\_processing.workflow.control\_reface module +------------------------------------------------ + +.. automodule:: func_processing.workflow.control_reface + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: func_processing.workflow + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/_build/html/_sources/index.rst.txt b/docs/_build/html/_sources/index.rst.txt index e4cb174..7c4780a 100644 --- a/docs/_build/html/_sources/index.rst.txt +++ b/docs/_build/html/_sources/index.rst.txt @@ -1,18 +1,17 @@ -.. emu-func-processing documentation master file, created by - sphinx-quickstart on Fri Mar 25 15:40:39 2022. +.. func_processing documentation master file, created by + sphinx-quickstart on Tue May 17 16:53:05 2022. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. -Welcome to emu-func-processing's documentation! -=============================================== +Welcome to func_processing's documentation! +=========================================== .. toctree:: - :maxdepth: 2 + :maxdepth: 3 :caption: Package Contents: modules - workflow - resources + func_processing Indices and tables diff --git a/docs/_build/html/_sources/modules.rst.txt b/docs/_build/html/_sources/modules.rst.txt index 11621e8..ff6e27c 100644 --- a/docs/_build/html/_sources/modules.rst.txt +++ b/docs/_build/html/_sources/modules.rst.txt @@ -4,6 +4,5 @@ func_processing .. toctree:: :maxdepth: 4 - resources + func_processing setup - workflow diff --git a/docs/_build/html/_sources/resources.afni.rst.txt b/docs/_build/html/_sources/resources.afni.rst.txt deleted file mode 100644 index c109060..0000000 --- a/docs/_build/html/_sources/resources.afni.rst.txt +++ /dev/null @@ -1,69 +0,0 @@ -resources.afni package -====================== - -Submodules ----------- - -resources.afni.copy module --------------------------- - -.. automodule:: resources.afni.copy - :members: - :undoc-members: - :show-inheritance: - -resources.afni.deconvolve module --------------------------------- - -.. automodule:: resources.afni.deconvolve - :members: - :undoc-members: - :show-inheritance: - -resources.afni.group module ---------------------------- - -.. automodule:: resources.afni.group - :members: - :undoc-members: - :show-inheritance: - -resources.afni.masks module ---------------------------- - -.. automodule:: resources.afni.masks - :members: - :undoc-members: - :show-inheritance: - -resources.afni.motion module ----------------------------- - -.. automodule:: resources.afni.motion - :members: - :undoc-members: - :show-inheritance: - -resources.afni.process module ------------------------------ - -.. automodule:: resources.afni.process - :members: - :undoc-members: - :show-inheritance: - -resources.afni.submit module ----------------------------- - -.. automodule:: resources.afni.submit - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: resources.afni - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/_build/html/_sources/resources.ashs.rst.txt b/docs/_build/html/_sources/resources.ashs.rst.txt deleted file mode 100644 index 4841e29..0000000 --- a/docs/_build/html/_sources/resources.ashs.rst.txt +++ /dev/null @@ -1,21 +0,0 @@ -resources.ashs package -====================== - -Submodules ----------- - -resources.ashs.hipseg module ----------------------------- - -.. automodule:: resources.ashs.hipseg - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: resources.ashs - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/_build/html/_sources/resources.fmriprep.rst.txt b/docs/_build/html/_sources/resources.fmriprep.rst.txt deleted file mode 100644 index 3bd12e8..0000000 --- a/docs/_build/html/_sources/resources.fmriprep.rst.txt +++ /dev/null @@ -1,21 +0,0 @@ -resources.fmriprep package -========================== - -Submodules ----------- - -resources.fmriprep.preprocess module ------------------------------------- - -.. automodule:: resources.fmriprep.preprocess - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: resources.fmriprep - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/_build/html/_sources/resources.reports.rst.txt b/docs/_build/html/_sources/resources.reports.rst.txt deleted file mode 100644 index 8d07234..0000000 --- a/docs/_build/html/_sources/resources.reports.rst.txt +++ /dev/null @@ -1,21 +0,0 @@ -resources.reports package -========================= - -Submodules ----------- - -resources.reports.check\_complete module ----------------------------------------- - -.. automodule:: resources.reports.check_complete - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: resources.reports - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/_build/html/_sources/workflow.rst.txt b/docs/_build/html/_sources/workflow.rst.txt deleted file mode 100644 index 5835d77..0000000 --- a/docs/_build/html/_sources/workflow.rst.txt +++ /dev/null @@ -1,45 +0,0 @@ -workflow package -================ - -Submodules ----------- - -workflow.control\_afni module ------------------------------ - -.. automodule:: workflow.control_afni - :members: - :undoc-members: - :show-inheritance: - -workflow.control\_ashs module ------------------------------ - -.. automodule:: workflow.control_ashs - :members: - :undoc-members: - :show-inheritance: - -workflow.control\_fmriprep module ---------------------------------- - -.. automodule:: workflow.control_fmriprep - :members: - :undoc-members: - :show-inheritance: - -workflow.control\_reface module -------------------------------- - -.. automodule:: workflow.control_reface - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: workflow - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/_build/html/_static/documentation_options.js b/docs/_build/html/_static/documentation_options.js index 2fa8c97..07966ec 100644 --- a/docs/_build/html/_static/documentation_options.js +++ b/docs/_build/html/_static/documentation_options.js @@ -1,6 +1,6 @@ var DOCUMENTATION_OPTIONS = { URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), - VERSION: '', + VERSION: '1.0', LANGUAGE: 'None', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/docs/_build/html/func_processing.html b/docs/_build/html/func_processing.html new file mode 100644 index 0000000..49f377b --- /dev/null +++ b/docs/_build/html/func_processing.html @@ -0,0 +1,168 @@ + + + + + + func_processing package — func_processing 1.0 documentation + + + + + + + + + + + + + + + +
+ + +
+ +
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+ +
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+ + + + \ No newline at end of file diff --git a/docs/_build/html/resources.afni.html b/docs/_build/html/func_processing.resources.afni.html similarity index 63% rename from docs/_build/html/resources.afni.html rename to docs/_build/html/func_processing.resources.afni.html index c80a351..8872aff 100644 --- a/docs/_build/html/resources.afni.html +++ b/docs/_build/html/func_processing.resources.afni.html @@ -3,7 +3,7 @@ - resources.afni package — emu-func-processing documentation + func_processing.resources.afni package — func_processing 1.0 documentation + + + + + + + + + + + + + +
+ + +
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+ + + + \ No newline at end of file diff --git a/docs/_build/html/resources.reports.html b/docs/_build/html/func_processing.resources.reports.html similarity index 58% rename from docs/_build/html/resources.reports.html rename to docs/_build/html/func_processing.resources.reports.html index b1d5b3a..bd053de 100644 --- a/docs/_build/html/resources.reports.html +++ b/docs/_build/html/func_processing.resources.reports.html @@ -3,7 +3,7 @@ - resources.reports package — emu-func-processing documentation + func_processing.resources.reports package — func_processing 1.0 documentation - - - - - - - - - - - - - -
- - -
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- - - - \ No newline at end of file diff --git a/docs/_build/html/search.html b/docs/_build/html/search.html index 39261b9..ac9008e 100644 --- a/docs/_build/html/search.html +++ b/docs/_build/html/search.html @@ -3,7 +3,7 @@ - Search — emu-func-processing documentation + Search — func_processing 1.0 documentation