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‎README.md

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![Junifer logo](docs/images/junifer_logo.png)
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![Junifer logo](docs/images/junifer_logo.png "junifer logo")
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# junifer - JUelich NeuroImaging FEature extractoR
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If you use junifer in a scientific publication, we would appreciate if you cite our work. Currently, we do not have a publication, so feel free to use the project [URL](https://juaml.github.io/junifer).
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## Funding
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We thank the [Helmholtz Imaging Platform](https://helmholtz-imaging.de/) and
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[SMHB](https://www.fz-juelich.de/en/smhb) for supporting development of Junifer.
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(The funding sources had no role in the design, implementation and evaluation of the pipeline.)
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## Contribution
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Contributions are welcome and greatly appreciated. Please read the [guidelines](https://juaml.github.io/junifer/main/contributing.html) to get started.

‎docs/changes/0.0.1.inc

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v0.0.1
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------
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Enhancements
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~~~~~~~~~~~~
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- Create the repository based on the mockup by `Fede Raimondo`_.
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- Implement :class:`junifer.testing.datagrabbers.SPMAuditoryTestingDatagrabber` datagrabber
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(:gh:`52` by `Fede Raimondo`_).
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- Add comments to :class:`junifer.datagrabber.DataladDataGrabber` datagrabber and change to
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use ``datalad-clone`` instead of ``datalad-install`` (:gh:`55` by `Benjamin Poldrack`_).
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- Add an example how to use junifer and julearn in one pipeline to extract features
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and do machine learning (:gh:`40` by `Leonard Sasse`_, `Nicolas Nieto`_, and `Sami Hamdan`_).
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- Implement matrix storage in SQliteFeatureStorage (:gh:`42` by `Fede Raimondo`_).
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- Implement :class:`junifer.markers.FunctionalConnectivityParcels` marker for functional
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connectivity using a parcellation (:gh:`41` by `Amir Omidvarnia`_ and `Kaustubh R. Patil`_).
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- Add documentation for the datagrabbers (by `Leonard Sasse`_,
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`Nicolas Nieto`_, and `Sami Hamdan`_).
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- Implement coordinate register, list and load (:gh:`11` by `Fede Raimondo`_).
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- Add :class:`junifer.datagrabber.DataladAOMICID1000` datagrabber for AOMIC ID1000 dataset
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including tests and creation of mock dataset for testing (:gh:`60` by `Vera Komeyer`_, `Xuan Li`_).
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- Add support to access other input in the data object in the ``compute`` method
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(by `Fede Raimondo`_).
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- Implement :class:`junifer.markers.RSSETSMarker` marker (:gh:`51` by `Leonard Sasse`_,
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`Nicolas Nieto`_, `Sami Hamdan`_).
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- Implement :class:`junifer.markers.SphereAggregation` marker (by `Fede Raimondo`_).
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- Implement :class:`junifer.datagrabber.DataladAOMICPIOP1` and
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:class:`junifer.datagrabber.DataladAOMICPIOP2` datagrabbers for AOMIC PIOP1 and PIOP2 datasets
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respectively and refactor :class:`junifer.datagrabber.DataladAOMICID1000` slightly
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(:gh:`94` by `Leonard Sasse`_)
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- Implement :class:`junifer.configs.juseless.datagrabbers.JuselessDataladCamCANVBM` datagrabber
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(:gh:`99` by `Leonard Sasse`_)
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- Implement :class:`junifer.configs.juseless.datagrabbers.JuselessDataladIXIVBM` CAT output
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datagrabber for juseless (:gh:`48` by `Leonard Sasse`_).
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- Upgrade storage interface for storage-like objects (:gh:`84` by `Synchon Mandal`_).
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- Add missing type annotations (:gh:`74` by `Synchon Mandal`_).
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- Add ``junifer wtf`` to report environment details (:gh:`33` by `Synchon Mandal`_).
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- Add ``junifer selftest`` to report environment details (:gh:`9` by `Synchon Mandal`_).
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- Refactor markers ``on`` attribute and ``get_valid_inputs`` to verify that the marker can
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be computed on the input data types (by `Fede Raimondo`_)
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- Implement :class:`junifer.configs.juseless.datagrabbers.JuselessDataladAOMICID1000VBM`
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datagrabber for accessing AOMIC ID1000 VBM from juseless (:gh:`57` by `Felix Hoffstaedter`_
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and `Synchon Mandal`_)
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- Add test for :class:`junifer.datagrabber.DataladHCP1200` datagrabber (:gh:`93` by `Synchon Mandal`_).
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- Change documentation template to furo. Fix references and standardize documentation (:gh:`114` by `Fede Raimondo`_).
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- Add :class:`junifer.preprocess.fMRIPrepConfoundRemover` (:gh:`111` by `Fede Raimondo`_ and `Leonard Sasse`_).
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- Implement :class:`junifer.markers.CrossParcellationFC` marker (:gh:`85` by `Leonard Sasse`_
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and `Kaustubh R. Patil`_)
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- Add :class:`junifer.configs.juseless.datagrabbers.JuselessUCLA` datagrabber for the UCLA dataset
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available on juseless (:gh:`118` by `Leonard Sasse`_).
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- Rename "atlas" to "parcellation" (:gh:`116` by `Fede Raimondo`_).
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- Refactor the :class:`junifer.datagrabber.BaseDataGrabber` class to allow for easier subclassing (:gh:`123` by `Fede Raimondo`_).
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- Allow custom aggregation method for :class:`junifer.markers.SphereAggregation` (:gh:`102` by `Synchon Mandal`_).
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- Add support for "masks" (:gh:`79` by `Fede Raimondo`_).
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- Allow :class:`junifer.markers.ParcelAggregation` to apply multiple parcellations at once (:gh:`131` by `Fede Raimondo`_).
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- Introduce a singleton decorator for marker computations (:gh:`151` by `Synchon Mandal`_).
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- Refactor :class:`junifer.pipeline.PipelineStepMixin` to improve its implementation and validation for pipeline steps
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(:gh:`152` by `Synchon Mandal`_).
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- Implement :class:`junifer.markers.ReHoParcels` and :class:`junifer.markers.ReHoSpheres` markers (:gh:`36` by `Synchon Mandal`_).
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- Implement :class:`junifer.markers.AmplitudeLowFrequencyFluctuationParcels` and
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:class:`junifer.markers.AmplitudeLowFrequencyFluctuationSpheres` markers (:gh:`35` by `Fede Raimondo`_).
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Bugs
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~~~~
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- Fix a bug in which a :class:`junifer.datagrabber.PatternDataGrabber` would now work with relative ``datadir`` paths.
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(:gh:`96` by `Leonard Sasse`_, fixed in :gh:`98` by `Fede Raimondo`_).
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- Fix a bug in which :class:`junifer.datagrabber.DataladAOMICPIOP2` datagrabber did not use user input to
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constrain elements based on tasks (:gh:`105` by `Leonard Sasse`_)
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- Fix a bug in which a datalad dataset could remove a user-cloned dataset (:gh:`53` by `Fede Raimondo`_)
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- Fix a bug in which CLI command would not work using elements with more than one field (by `Fede Raimondo`_).
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- Fix a bug in which the generated DAG for HTCondor will not work (:gh:`143` by `Fede Raimondo`_).
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API changes
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~~~~~~~~~~~
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- Change the ``single_output`` default parameter in storage classes from ``False`` to ``True`` (:gh:`134` by `Fede Raimondo`_).

‎docs/changes/latest.inc

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.. _current:
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Current (0.0.0.dev)
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Current (0.0.2.dev)
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-------------------
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Enhancements
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~~~~~~~~~~~~
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- Created a the repository based on the mockup by `Fede Raimondo`_.
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- Implemented SPM Auditory testing datagrabber X (:gh:`52` by `Fede Raimondo`_).
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- Added comments to datalad grabber and changed to use datalad-clone instead of
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datalad-install (:gh:`55` by `Benjamin Poldrack`_).
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- Added an example how to use junifer and julearn (:gh:`40` by `Leonard Sasse`_,
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`Nicolas Nieto`_, and `Sami Hamdan`_) in one pipeline to extract features
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and do machine learning.
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- Implement matrix storage in SQliteFeatureStorage (:gh:`42` by `Fede Raimondo`_).
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- Marker for functional connectivity using a parcellation (:gh:`41` by
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`Amir Omidvarnia`_ and `Kaustubh R. Patil`_).
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- Added documentation for the datagrabbers (by `Leonard Sasse`_,
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`Nicolas Nieto`_, and `Sami Hamdan`_).
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- Implement coordinate register, list and load (:gh:`11` by `Fede Raimondo`_).
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- Added datagrabber for AOMIC1000 dataset including tests and creation of mock
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dataset for testing (:gh:`60` by `Vera Komeyer`_, `Xuan Li`_).
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- Added support to access other input in the data object in the `compute` method
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(by `Fede Raimondo`_).
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- Implemented the edge time series RSS marker (:gh:`51` by `Leonard Sasse`_,
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`Nicolas Nieto`_, `Sami Hamdan`_).
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- Implement SphereAggregation marker (by `Fede Raimondo`_).
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- Implement PIOP1 and PIOP2 AOMIC datasets and refactor AOMICID1000 slightly
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(:gh:`94` by `Leonard Sasse`_)
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- Implement a JuselessDataladCamCANVBM datagrabber class (:gh:`99` by `Leonard Sasse`_)
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- Implement IXI CAT output datagrabber for juseless (:gh:`48` by `Leonard Sasse`_).
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- Upgrade storage interface for storage-like objects (:gh:`84` by `Synchon Mandal`_).
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- Add missing type annotations (:gh:`74` by `Synchon Mandal`_).
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- Add ``junifer wtf`` to report environment details (:gh:`33` by `Synchon Mandal`_).
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- Add ``junifer selftest`` to report environment details (:gh:`9` by `Synchon Mandal`_).
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- Refactor markers ``on`` attribute and ``get_valid_inputs`` to verify that the marker can be computed on the input data types (by `Fede Raimondo`_)
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- Implement JuselessDataladAOMICID1000VBM datagrabber for accessing AOMIC ID 1000 VBM from juseless (:gh:`57` by `Felix Hoffstaedter`_ and `Synchon Mandal`_)
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- Add test for DataladHCP1200 datagrabber (:gh:`93` by `Synchon Mandal`_).
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- Change documentation template to furo. Fix references and standardize documentation (:gh:`114` by `Fede Raimondo`_).
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- Add :class:`junifer.preprocess.fMRIPrepConfoundRemover` (:gh:`111` by `Fede Raimondo`_ and `Leonard Sasse`_).
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- Implement CrossParcellationFC marker (:gh:`85` by `Leonard Sasse`_ and `Kaustubh R. Patil`_)
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- Add datagrabber implementation for the UCLA dataset available on juseless (:gh:`118` by `Leonard Sasse`_).
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- Rename "atlas" to "parcellation" (:gh:`116` by `Fede Raimondo`_).
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- Refactor the :class:`junifer.datagrabber.BaseDataGrabber` class to allow for easier subclassing (:gh:`123` by `Fede Raimondo`_).
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- Allow custom aggregation method for :class:`junifer.markers.SphereAggregation` (:gh:`102` by `Synchon Mandal`_).
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- Add support for "masks" (:gh:`79` by `Fede Raimondo`_).
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- Allow :class:`junifer.markers.ParcelAggregation` to apply multiple parcellations at once (:gh:`131` by `Fede Raimondo`_).
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- Introduce a singleton decorator for marker computations (:gh:`151` by `Synchon Mandal`_).
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- Refactor :class:`junifer.pipeline.PipelineStepMixin` to improve its implementation and validation for pipeline steps
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(:gh:`152` by `Synchon Mandal`_).
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- Implement :class:`junifer.markers.ReHoParcels` and :class:`junifer.markers.ReHoSpheres` markers (:gh:`36` by `Synchon Mandal`_).
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- Implement :class:`junifer.markers.AmplitudeLowFrequencyFluctuationParcels` and :class:`junifer.markers.AmplitudeLowFrequencyFluctuationSpheres` markers (:gh:`35` by `Fede Raimondo`_).
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Bugs
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~~~~
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- Fix a bug in which a PatternDatagrabber would now work with relative `datadir` paths.
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(:gh:`96` by `Leonard Sasse`_, fixed in :gh:`98` by `Fede Raimondo`_).
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- Fix a bug in which AOMIC PIOP2 datagrabber did not use user input to constrain elements based on tasks (:gh:`105` by `Leonard Sasse`_)
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- Fix a bug in which a datalad dataset could remove a user-cloned dataset (:gh:`53` by `Fede Raimondo`_)
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- Fix a bug in which CLI command would not work using elements with more than one field (by `Fede Raimondo`_).
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- Fix a bug in which the generated DAG for HTCondor will not work (:gh:`143` by `Fede Raimondo`_).
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API changes
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~~~~~~~~~~~
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- Change the ``single_output`` default parameter in storage classes from ``False`` to ``True`` (:gh:`134` by `Fede Raimondo`_).

‎docs/index.rst

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* :ref:`genindex`
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* :ref:`modindex`
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* :ref:`search`
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Funding
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=======
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We thank the `Helmholtz Imaging Platform <https://helmholtz-imaging.de/>`_ and
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`SMHB <https://www.fz-juelich.de/en/smhb>`_ for supporting development of Junifer.
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(The funding sources had no role in the design, implementation and evaluation of the pipeline.)

‎docs/installation.rst

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AFNI
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----
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To install AFNI, you can always follow the `AFNI official instructions
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To install AFNI, you can always follow the `AFNI official instructions
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<https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/main_toc.html>`_. Additionally, you can also follow
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the following steps to install and configure the AFNI Docker container in your local system.
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.. important::
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.. important::
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The AFNI Docker container wrappers add the commands required by Junifer. Using this commands have
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some limitations, mostly related to handling files and paths. Junifer knows about this and uses this
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commands in the proper way. Keep this in mind if you try to use the AFNI Docker wrappers outside of junifer. This
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caveats and limitations are not documented.
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The AFNI Docker container wrappers add the commands required by junifer. Using these commands have
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some limitations, mostly related to handling files and paths. Junifer knows about this and uses these
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commands in the proper way. Keep this in mind if you try to use the AFNI Docker wrappers outside of junifer.
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These caveats and limitations are not documented.
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1. Install Docker. You can follow the `Docker official instructions <https://docs.docker.com/get-docker/>`_.
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2. Pull the AFNI Docker image from `Docker Hub <https://hub.docker.com/r/afni/afni>`_:
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junifer setup afni-docker
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Take the last line and copy it to your ``.bashrc`` or ``.zshrc`` file.
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Take the last line and copy it to your ``.bashrc`` or ``.zshrc`` file.
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Or, alternatively, you can exceute this command which will update the ``~/.bashrc`` for you:
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‎docs/maintaining.rst

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The CI scripts will publish every tag with the format *v.X.Y.Z* to Pypi as
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version "X.Y.Z". Additionally, for every push to main, it will be published
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as pre-release to TestPypi.
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as pre-release to PyPI.
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Releasing a new version
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git tag -a vD.E.0.dev -m "Set next release to D.E.0"
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git push origin --follow-tags
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‎docs/whats_new.rst

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==========
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.. include:: changes/latest.inc
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.. include:: changes/0.0.1.inc
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.. include:: changes/contributors.inc
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.. include:: links.inc
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.. include:: links.inc

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