diff --git a/data/tools/converters.yml b/data/tools/converters.yml index 4dfaefad..98ce60ea 100644 --- a/data/tools/converters.yml +++ b/data/tools/converters.yml @@ -2,6 +2,7 @@ # template # - name: # url: URL to repo +# status: active # data_types: # - MRI, EEG, MEG, iEEG, events, physio # expected_input: @@ -20,6 +21,7 @@ - name: AFNI BIDS-tools url: https://github.com/nih-fmrif/BIDS-tools + status: archived data_types: - MRI expected_input: @@ -31,6 +33,7 @@ - name: Autobids url: https://github.com/khanlab/autobids + status: archived data_types: - MRI expected_input: @@ -44,6 +47,7 @@ - name: BIDS2ISATab url: https://github.com/bids-standard/BIDS2ISATab + status: active data_types: - BIDS expected_input: @@ -55,6 +59,7 @@ - name: BIDS2NDA url: https://github.com/bids-standard/BIDS2NDA + status: active data_types: - BIDS expected_input: @@ -64,20 +69,9 @@ comment: Extract NIHM Data Archive compatible metadata from BIDS license: Apache-2.0 -- name: BIDS2NIDM - url: https://github.com/incf-nidash/PyNIDM/blob/master/nidm/experiment/tools/nidm2bids.py - data_types: - - BIDS - expected_input: - - BIDS - language: - - Python - comment: | - This program will convert a NIDM-Experiment RDF document to a BIDS - dataset. - - name: BIDScoin url: https://github.com/Donders-Institute/bidscoin + status: active data_types: - MRI - physiological @@ -107,6 +101,7 @@ - name: BIDSconvertR url: https://github.com/bidsconvertr/bidsconvertr + status: active comment: | The BIDSconvertR R package provides a user-friendly workflow with graphical user interfaces. It consists of the following steps: @@ -125,6 +120,7 @@ - name: BIDSme url: https://github.com/nbeliy/bidsme + status: active data_types: - MRI - EEG @@ -140,6 +136,7 @@ - name: BIDSto3col url: https://github.com/bids-standard/bidsutils/tree/master/BIDSto3col + status: active data_types: - TSV expected_input: @@ -151,6 +148,7 @@ - name: BMAT url: https://github.com/ColinVDB/BMAT + status: active data_types: - MRI expected_input: @@ -165,6 +163,7 @@ - name: Biscuit url: https://github.com/Macquarie-MEG-Research/Biscuit + status: active data_types: - MEG expected_input: @@ -178,6 +177,7 @@ - name: BrkRaw url: https://github.com/BrkRaw/brkraw + status: active data_types: - MRI expected_input: @@ -190,6 +190,7 @@ - name: Clinica url: https://github.com/aramis-lab/clinica + status: active data_types: - MRI # not sure expected_input: @@ -206,6 +207,7 @@ - name: Data2Bids url: https://github.com/SIMEXP/Data2Bids + status: active data_types: - MRI expected_input: @@ -222,6 +224,7 @@ - name: Dcm2Bids url: https://github.com/cbedetti/Dcm2Bids + status: active data_types: - MRI expected_input: @@ -239,6 +242,7 @@ - name: EEG2BIDS url: https://github.com/aces/EEG2BIDS + status: active data_types: - EEG expected_input: @@ -252,6 +256,7 @@ - name: EEGLAB url: https://github.com/sccn/eeglab + status: active data_types: - MEG - EEG @@ -267,6 +272,7 @@ - name: Explore ASL url: https://github.com/ExploreASL/ExploreASL + status: active comment: | Convert DICOM and NIFTI data to the ASL-BIDS format. data_types: @@ -281,6 +287,7 @@ - name: FieldTrip - data2bids url: https://github.com/fieldtrip/fieldtrip + status: active data_types: - EEG - MEG @@ -299,6 +306,7 @@ - name: HeuDiConv url: https://github.com/nipy/heudiconv + status: active data_types: - MRI expected_input: @@ -318,6 +326,7 @@ - name: Horos (Osirix) export plugin url: https://github.com/mslw/horos-bids-output + status: active data_types: - MRI # not sure expected_input: @@ -330,6 +339,7 @@ - name: MNE-BIDS url: https://github.com/mne-tools/mne-bids + status: active data_types: - MEG - EEG @@ -355,6 +365,7 @@ - name: OpenfMRI2BIDS url: https://github.com/bids-standard/openfmri2bids + status: active data_types: - MRI # not sure expected_input: @@ -365,6 +376,7 @@ - name: PET2BIDS url: https://github.com/openneuropet/PET2BIDS + status: active comment: | Helps you convert your PET data! raw PET scanner files (for example ecat, dicom) and additional side file like excel sheets. @@ -381,6 +393,7 @@ - name: ReproIn url: https://github.com/ReproNim/reproin + status: active data_types: - MRI expected_input: @@ -395,6 +408,7 @@ - name: SAMRI url: https://github.com/IBT-FMI/SAMRI + status: active comment: | Full stack Small Animal MRI data analysis package, including the `bru2bids` repositing pipeline, which can convert Bruker archives to the BIDS format. @@ -409,11 +423,12 @@ language: - Python - shell - documentation: https://doi.org/10.3389/fninf.2020.00005 + article: https://doi.org/10.3389/fninf.2020.00005 GUI: false - name: XNAT2BIDS url: https://github.com/kamillipi/2bids + status: active data_types: - MRI # not sure expected_input: @@ -426,8 +441,9 @@ - name: bids2xar - for XNAT import url: https://github.com/lwallace23/bids2xar + status: active data_types: - - MRI # not sure + - BIDS expected_input: - BIDS language: @@ -436,6 +452,7 @@ - name: bidsify url: https://github.com/NILAB-UvA/bidsify + status: archived data_types: - MRI expected_input: @@ -452,6 +469,7 @@ - name: bidskit url: https://github.com/jmtyszka/bidskit + status: active data_types: - MRI expected_input: @@ -469,6 +487,7 @@ - name: bidsphysio url: https://github.com/cbinyu/bidsphysio + status: active data_types: - physiological expected_input: @@ -488,6 +507,7 @@ - name: convert-eprime url: https://github.com/tsalo/convert-eprime + status: active data_types: - MISC - behavioral @@ -500,6 +520,7 @@ - name: dac2bids url: https://github.com/dangom/dac2bids + status: active data_types: - MRI expected_input: @@ -510,6 +531,7 @@ - name: ezBIDS url: https://github.com/brainlife/ezbids + status: active data_types: - MRI - ASL @@ -537,6 +559,7 @@ - name: mercure-dcm2bids url: https://github.com/mercure-imaging/mercure-dcm2bids + status: active data_types: - MRI expected_input: @@ -559,6 +582,7 @@ - name: niix2bids url: https://github.com/benoitberanger/niix2bids + status: active data_types: - MRI # not sure expected_input: @@ -570,6 +594,7 @@ - name: phys2bids url: https://github.com/physiopy/phys2bids + status: active data_types: - phsyiological expected_input: @@ -587,6 +612,7 @@ - name: sim2bids url: https://github.com/dissagaliyeva/sim2bids + status: active data_types: - MISC - computational model @@ -600,8 +626,10 @@ comment: GUI to easily convert simulation results to BIDS format, according to BEP 34 . license: MIT + - name: sovabids url: https://github.com/yjmantilla/sovabids + status: active data_types: - EEG expected_input: diff --git a/macros/macros.py b/macros/macros.py index 75759b7a..5a007a0e 100644 --- a/macros/macros.py +++ b/macros/macros.py @@ -124,7 +124,7 @@ def filename_template_for(schema_obj, datatype): def main(): - print(generate_filename_templates()) + print(generate_converter_table(file="converters.yml", data_type="MRI")) if __name__ == "__main__": diff --git a/templates/converters_table_md.jinja b/templates/converters_table_md.jinja index c1ba3717..de87bb76 100644 --- a/templates/converters_table_md.jinja +++ b/templates/converters_table_md.jinja @@ -1,7 +1,7 @@ | Name | Expected input | Language | Distribution | Updated | | :---: | :------------ | :------ | :---------- | :-----: | {% for converter in include %} - {% if data_type in converter.data_types %} + {% if converter.status == 'active' and data_type in converter.data_types %} {% if data_type in converter.data_types %} {% set converter_url = converter.documentation if converter.documentation else converter.url %} | [{{ converter.name }}]( {{ converter_url }} "{{ converter.comment | replace("\n", " ") }}" ) | {% for input in converter.expected_input or ["N/A"] %} {{ input }}
{% endfor %} | {% for lang in converter.language or ["N/A"] %} {{ lang }}
{% endfor %} | {% for entry in converter.distribution or [] %} {% if entry.name == "pypi" %} [![PyPI version](https://badge.fury.io/py/{{ entry.url | replace("https://pypi.org/project/", "") }}.svg)]({{ entry.url }})
{% elif entry.name == "dockerhub" %} [![dockerhub pulls](https://img.shields.io/docker/pulls/{{ entry.url | replace("https://hub.docker.com/r/", "")}}.svg)]({{ entry.url }})
{% elif entry.name == "conda-forge" %} [![conda forge]({{ entry.url }}badges/version.svg)]({{ entry.url }})
{% else %} [entry.name](entry.url)
{% endif %} {% endfor %} | !["GitHub last commit"](https://img.shields.io/github/last-commit/{{ converter.url | replace("https://github.com/", "") }}?style=plastic) |