[ENH] Add Glossary of terms/abbreviations used in the specification #152

yarikoptic · 2019-02-15T17:48:15Z

Just an idea which came up while fighting over the suffix in PyBIDS: bids-standard/pybids#380

BTW -- does anyone know about a proper way to define glossary and refer to the terms in this markdown/mkdocs, like e.g. :term: in sphinx?

chrisgorgo · 2019-02-19T18:44:05Z

Thank you for sending this over. How do you see the proposed glossary overlapping with Definitions outlined in Common Principles - https://github.com/bids-standard/bids-specification/blob/master/src/02-common-principles.md#definitions ? Perhaps it's worth extending that section instead of creating a new one. Curious about your thoughts.

yarikoptic · 2019-02-19T21:03:34Z

Great question, and shame on me that I forgot about them being listed there. I would be happy to contribute to it instead. What is left is file extension, <index>, <label>, suffix. They sound a bit too "down to the earth/detail" in comparison to the other more prominent high level definitions. But I think they would be appropriate since they are used through the spec. Just gimme the blessing Father! ;)

May be that is a part of the problem, that it is somewhat buried within the common principles instead of separate section? I have no strong opinion on this one

chrisgorgo · 2019-02-19T21:06:02Z

What if the compromise would be to have a dedicated "definitions/glossary" section early on in the spec (instead of the appendix)?

KirstieJane · 2019-02-20T07:34:38Z

Little +1 on @chrisfilo’s idea - I think the definitions are really useful and putting them in the appendix makes them harder to find for new folks.

yarikoptic · 2019-05-09T13:30:36Z

Mental buzz to myself to get back to it to refurbish to come earlier. Kept running into absence of clear description for the <index> and <label> and common principle is indeed the place them to be listed. If someone beats me to do it -- I would only appreciate

yarikoptic · 2019-05-09T13:32:25Z

src/99-appendices/09-glossary.md

+   indentation, e.g. it is `01` in `run-01` following `run-<index>` specification
+- **<label>**:
+   an alphanumeric value, possibly prefixed with arbitrary number of 0s for consistent
+   indentation, e.g. it is `rest` in `task-rest` following `task-<label>` specification


me whining: I am so desperately waiting for - or + to become allowed! in case of derivatives _desc it is quite hard to provide it sometimes without any way to punctuate items

Also added consistency in referencing "resting state" task

…<label>s and <index>es

yarikoptic · 2019-05-10T01:38:33Z

ok, pushed (rebased) updates placing <index> and <label> into Definitions and then rewording/shortening section describing loose term "labels". I also added some formatting to make Definitions IMHO easier to parse/link to each other

sappelhoff

Thanks @yarikoptic ... just a small comment, otherwise LGTM

sappelhoff · 2019-05-10T06:58:44Z

src/02-common-principles.md

+
+1.  **File extension** - a portion of the the file name after the left-most
+    period (`.`) preceded by any other alphanumeric (so `.gitignore` does not have a
+    suffix)


do you mean the right-most period? Also, the .gitignore example is not clear to me: Why is the suffix of relevance when describing what a file extension is?

Left-most is correct. Following the right-most rule for X.nii.gz would get you .gz, not .nii.gz.

By this definition, .func.gii, .surf.gii and .dtseries.nii are extensions, which I think is appropriate, but we should make sure we're on the same page here, as these are part of derivatives.

re .gitignore -- just an example where there is a left-most period but the gitignore is not an extension because is not preceded by anything. May be I should replace it with .bidsignore, which is also not a part of the spec but more relevant here?

@effigies you bring up the point either period itself is a part of file extension, i.e. either it is .nii.gz or nii.gz?!

in my wording above it is without ("... after ...") so might need to be fixed.

Python seems to also retain period in splitext:

$> python -c 'from os.path import splitext; print(splitext("bla.nii.gz"))' ('bla.nii', '.gz')

text in bids-specification ATM seems to list them with period (IMHO makes it easier to parse when period is there)

pybids seems to ask for them without period (might be my influence attn: @tyarkoni :

(git)hopa:~/proj/bids/pybids[sqlalchemy]git $> git grep extension.*nii bids/layout/README.md:>>> files = layout.get(subject='0[12]', run=1, extension='.nii.gz') bids/layout/README.md:In the above snippet, we retrieve all files with subject id 1 or 2 and run id 1 (notice that any entity defined in the config file can be used a filtering argument), and with a file extension of .nii.gz. The returned result is a list of named tuples, one per file, allowing direct access to the defined entities as attributes. bids/layout/config/bids.json: "sub-{subject}[/ses-{session}]/dwi/sub-{subject}[_ses-{session}][_acq-{acquisition}]_{suffix<dwi>}{extension<bval|bvec|json|nii\\.gz|nii>|nii\\.gz}", bids/layout/index.py: extension=['nii', 'nii.gz'], suffix='bold', bids/layout/index.py: extension=['nii', 'nii.gz'], suffix='dwi', bids/layout/layout.py: extension=['nii.gz', 'nii']) bids/layout/layout.py: images = self.get(extension=['nii', 'nii.gz'], scope=scope, bids/layout/tests/test_layout.py: 'extension': 'nii.gz'} bids/layout/tests/test_layout.py: 'desc': 'bleargh', 'extension': 'nii.gz'} bids/layout/tests/test_layout.py: 'extension': 'nii.gz'} bids/layout/tests/test_layout.py: 'desc': 'bleargh', 'extension': 'nii.gz'} bids/layout/tests/test_layout.py: acquisition='fullbrain', extension='nii.gz')[0] bids/reports/parsing.py: iff_file = [f for f in layout.get(extension='nii.gz') if fn in f.path][0] bids/reports/parsing.py: echos = layout.get_echoes(subject=subj, extension='nii.gz', bids/reports/parsing.py: extension='nii.gz', bids/reports/report.py: niftis = self.layout.get(subject=subject, extension='nii.gz', bids/reports/tests/test_parsing.py: niftis = testlayout.get(subject=subj, extension='nii.gz') bids/variables/io.py: images = layout.get(return_type='object', extension='nii.gz', doc/layout/index.rst: >>> f = layout.get(task='nback', run=1, extension='nii.gz')[0].filename doc/layout/index.rst: >>> f = layout.get(task='nback', run=1, extension='nii.gz')[0].filename examples/pybids tutorial.ipynb: "layout.get(subject='01', extension='nii.gz', suffix='bold', return_type='filename')" examples/pybids tutorial.ipynb: "{'subject': '01', 'run': 1, 'suffix': 'T2w', 'extension': 'nii.gz'}" 1 11544.....................................:Fri 10 May 2019 08:53:36 AM EDT:. (git)hopa:~/proj/bids/pybids[sqlalchemy]git $> git describe 0.7.1-256-g52c6a7f

so what should it be? ;)

I think that the example should be "so sub-01_task-resting_bold.nii.gz has the suffix .nii.gz"

suffix should be bold. Extension nii.gz in current wording.

NB it has been awhile for this issue/PR, I might be loosing grip on what should be what now ;)

effigies · 2019-05-10T13:11:06Z

@yarikoptic re dots, I don't really care, and I wasn't trying to stake a position here. I can work with either, and I think any good tool will probably have to have a special case to check for missing/spurious initial dots.

yarikoptic · 2019-05-10T14:48:16Z

@yarikoptic re dots, I don't really care, and I wasn't trying to stake a position here. I can work with either, and I think any good tool will probably have to have a special case to check for missing/spurious initial dots.

yeah, but IMHO consistency between/within BIDS and terms used by "BIDS tools" is important, that is why I wonder myself now what should it be, even though it might sound like a superficial concern. But I am ok to postpone its further discussion until later/separate issue, or even remove "File extension" from this PR. Please advise.

sappelhoff · 2019-05-11T07:07:44Z

mmh 😕 ... both with or without a dot sounds fine. Just from my intuition, perhaps we can go with a dot in our definition here? It's probably better to make a strong definition (as opposed to "do whatever you want"), because it will make it easier for downstream tools to work with it.

In the spec, we are using extensions WITH a dot in several places:

tyarkoni · 2019-05-11T13:44:56Z

I'd rather make a decision on this now, because PyBIDS 0.9 (to be released imminently) already changes extensions to extension, so this is the optimal time to introduce a (possible) change to the pattern. My current plan was to switch from including the period to not including it, but maintain backward compatibility for a couple of version releases. But it would be bad to ask people to switch and then revert again later, so we should probably decide sooner rather than later.

Alternatively, I could say nothing about it and handle both scenarios, but that seems suboptimal for the reason @yarikoptic articulated (and even if we continue to handle both cases gracefully, there should probably be an official statement one way or the other that we can appeal to if needed).

sappelhoff · 2020-05-18T08:20:44Z

Having talked about definitions of label and index in the past weeks, I think this PR would be nice to get into the spec because it clarifies several parts.

Do you see any blockers @franklin-feingold @effigies?

Especially with regards to pybids?

franklin-feingold

looks good to me! this should help clarify this ambiguity

yarikoptic · 2020-05-19T15:25:12Z

woohoo -- we got an approval! BTW since the last time we discussed extension, pybids now seems consistently not include that leading .

so current description would stand:

$> git grep extension.*nii
bids/layout/config/bids.json:        "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio>}.{extension<nii|nii.gz|json>|nii.gz}",
bids/layout/config/bids.json:        "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_mod-{modality}]_{suffix<defacemask>}.{extension<nii|nii.gz|json>|nii.gz}",
bids/layout/config/bids.json:        "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}]_{suffix<bold|cbv|phase|sbref>}.{extension<nii|nii.gz|json>|nii.gz}",
bids/layout/config/bids.json:        "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}]_{suffix<dwi>}.{extension<bval|bvec|json|nii.gz|nii>|nii.gz}",
bids/layout/config/bids.json:        "sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_run-{run}]_{fmap<phasediff|magnitude[12]|phase[12]|fieldmap>}.{extension<nii|nii.gz|json>|nii.gz}",
bids/layout/config/bids.json:        "sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}]_dir-{direction}[_run-{run}]_{fmap<epi>}.{extension<nii|nii.gz|json>|nii.gz}",
bids/layout/index.py:                    extension=['nii', 'nii.gz'], suffix='bold',
bids/layout/index.py:                    extension=['nii', 'nii.gz'], suffix='dwi',
bids/layout/layout.py:                         extension=['nii.gz', 'nii'])
bids/layout/layout.py:        images = self.get(extension=['nii', 'nii.gz'], scope=scope,
bids/layout/tests/test_layout.py:        (False, {'task': 'rest', 'extension': ['nii.gz']}, 3.0),
bids/layout/tests/test_layout.py:        (False, {'task': 'rest', 'extension': 'nii.gz'}, 3.0),
bids/layout/tests/test_layout.py:        (False, {'task': 'rest', 'extension': ['nii.gz', 'json'], 'return_type': 'file'}, 3.0),
bids/layout/tests/test_layout.py:    sample_file = layout.get(task='rest', extension='nii.gz',
bids/layout/tests/test_layout.py:              'extension': 'nii.gz'}
bids/layout/tests/test_layout.py:              'desc': 'bleargh', 'extension': 'nii.gz'}
bids/layout/tests/test_layout.py:              'extension': 'nii.gz'}
bids/layout/tests/test_layout.py:              'desc': 'bleargh', 'extension': 'nii.gz'}
bids/layout/tests/test_layout.py:                            acquisition='fullbrain', extension='nii.gz')[0]
bids/layout/tests/test_layout.py:                    acquisition='fron.al', extension='nii.gz',
bids/layout/tests/test_layout.py:                    acquisition='fron.al', extension='nii.gz',
bids/layout/tests/test_layout.py:                    acquisition='fullbrain', extension='nii.gz',
bids/layout/tests/test_writing.py:        assert _PATTERN_FIND.findall('{extension<nii|nii.gz|json>|nii.gz}') == [
bids/layout/tests/test_writing.py:            ('{extension<nii|nii.gz|json>|nii.gz}', 'extension', 'nii|nii.gz|json', 'nii.gz')
bids/layout/tests/test_writing.py:{extension<nii|nii.gz|json>|nii.gz}"""
bids/layout/tests/test_writing.py:            ('{extension<nii|nii.gz|json>|nii.gz}', 'extension', 'nii|nii.gz|json', 'nii.gz'),
bids/layout/tests/test_writing.py:            assert build_path({'session': 'B', 'run': 3, 'extension': '.nii'},
bids/layout/tests/test_writing.py:        assert build_path({'session': 'B', 'run': 3, 'extension': '.nii'},
bids/layout/tests/test_writing.py:            "[_acq-{acquisition}]_{suffix|dwi}.{extension<bval|bvec|json|nii.gz|nii>|nii.gz}"
bids/layout/tests/test_writing.py:        pats = ['ses-{session<A|B|C>|D}/r-{run}.{extension<json|nii|nii.gz>|nii.gz}']
bids/layout/tests/test_writing.py:                'extension': ['.nii.gz', 'json']
bids/layout/writing.py:    ...     'extension': 'nii',
bids/layout/writing.py:    ...             'inplaneT[12]|angio>}.{extension<nii|nii.gz|json>|nii.gz}',
bids/layout/writing.py:    ...             '{extension<nii|nii.gz|json>|nii.gz}']
bids/layout/writing.py:    ...     "[_acq-{acquisition}]_{suffix|dwi}.{extension<bval|bvec|json|nii.gz|nii>|nii.gz}"
bids/reports/parsing.py:            iff_file = [f for f in layout.get(extension=[".nii", ".nii.gz"]) if fn in f.path][0]
bids/reports/parsing.py:                    echos = layout.get_echoes(subject=subj, extension=[".nii", ".nii.gz"],
bids/reports/parsing.py:                                                     extension=[".nii", ".nii.gz"],
bids/reports/report.py:        >>> files = layout.get(session='01', extension=['nii.gz', 'nii'])
bids/reports/report.py:                subject=subject, extension=[".nii", ".nii.gz"],
bids/reports/tests/test_parsing.py:    niftis = testlayout.get(subject=subj, extension=[".nii", ".nii.gz"])
bids/reports/tests/test_report.py:    files = testlayout.get(extension=['nii.gz', 'nii'])
bids/variables/io.py:    images = layout.get(return_type='object', extension='nii.gz',
doc/layout/index.rst:    >>> f = layout.get(task='nback', run=1, extension='nii.gz')[0].filename
doc/layout/index.rst:    >>> f = layout.get(task='nback', run=1, extension='nii.gz')[0].filename
examples/pybids_tutorial.ipynb:    "layout.get(subject='01', extension='nii.gz', suffix='bold', return_type='filename')"
examples/pybids_tutorial.ipynb:       "{'subject': '01', 'run': 1, 'suffix': 'T2w', 'extension': 'nii.gz'}"

Let me know merge master and resolve the conflicts and push...

* origin/master: (404 commits) [DOC] Auto-generate changelog entry for PR bids-standard#460 Apply suggestions from code review label -> index drop _part-, introduce _split- [DOC] Auto-generate changelog entry for PR bids-standard#459 [DOC] Auto-generate changelog entry for PR bids-standard#465 fix table Update src/99-appendices/06-meg-file-formats.md [DOC] Auto-generate changelog entry for PR bids-standard#441 inject _part into MEG spec update entity table FIX: clarify _part Apply suggestions from code review FIX: clarify participants tsv [DOC] Auto-generate changelog entry for PR bids-standard#457 Update Release_Protocol.md add pdf steps for release protocol FIX: remove BESA from list of restricted keywords Remove trailing space Add reference to PDF on front page of specification ... Conflicts: src/02-common-principles.md - had to meld with my previous wording etc.

yarikoptic · 2020-05-19T15:59:57Z

uff... merge conflict was a bit painful, so probably a nice look through the diff would not hurt.

sappelhoff

I left some suggestions, but overall I'd be happy to get this in soon. Thank for rebasing @yarikoptic

src/02-common-principles.md

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

This would - match current use of "extension" in BIDS text - match use within bids-validator messages - stay inline with filename splitting utilities available in Python and Matlab Note: it is different from PyBIDS which ATM does not require leading '.' for `extension` specification in the queries. Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

yarikoptic · 2020-05-22T16:30:56Z

and ready for another round of review/recommendations and/or merge ;)

sappelhoff

https://github.com/bids-standard/bids-specification/pull/152/files#r429333329 is my last comment, other than that I approve.

But before we can merge, I'd like @effigies to have a look.

…uniqueness Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

* origin/master: [DOC] Auto-generate changelog entry for PR bids-standard#477 Also ignore users urls on github Quote regexp in command line [INFRA] linkchecker - ignore github pull and tree URLs

yarikoptic · 2020-05-22T19:50:44Z

ok, with a merge of recent master linkchecker is quiet, it is all green and just awaits another review from @effigies ;)

effigies

This looks good. Thanks for doing this @yarikoptic!

I think the wording around suffix can be made a little clearer (see suggestion).

Also notifying @tyarkoni that here extension is defined to include the initial .. PyBIDS currently transparently parses either, but when queried, returns without the ..

src/02-common-principles.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

yarikoptic · 2020-05-22T20:53:30Z

Now that accepted suggestion from @effigies , pr needs to be reapproved @sappelhoff

yarikoptic · 2020-05-22T20:57:12Z

Re pybids, filed bids-standard/pybids#618

* upstream/master: (113 commits) [DOC] Auto-generate changelog entry for PR bids-standard#152 [DOC] Auto-generate changelog entry for PR bids-standard#467 Specify that suffix must be alphanumeric ENH: make NOT RECOMMENDED stronger (SHOULD NOT) for zero padding for uniqueness ENH: Include leading . within definition of the file extension ENH: provide an example for a suffix based on an _eeg.vhdr filename [DOC] Auto-generate changelog entry for PR bids-standard#477 [DOC] Auto-generate changelog entry for PR bids-standard#460 Also ignore users urls on github Quote regexp in command line [INFRA] linkchecker - ignore github pull and tree URLs Apply suggestions from code review replace purview with scope label -> index Apply suggestions from code review drop _part-, introduce _split- Apply SA feedback and amended to purview [DOC] Auto-generate changelog entry for PR bids-standard#459 Add Domain Expert to Maintainers Group [DOC] Auto-generate changelog entry for PR bids-standard#465 ...

sappelhoff changed the title ~~ENH: Add Glossary of terms/abbreviations used in the specification~~ [ENH] Add Glossary of terms/abbreviations used in the specification Apr 12, 2019

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ENH: Add Glossary of terms/abbreviations used in the specification

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yarikoptic added 3 commits May 9, 2019 21:36

RF: move glossary terms into common principles definitions

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ENH: use formatting (**, ``) for Terms/Abbreviations items

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Also added consistency in referencing "resting state" task

RF: reword/shorten "Participant names and other labels" referring to …

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…<label>s and <index>es

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BF: missing period before {extension} group for some dwi/ files bids-standard/pybids#439

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[FIX] Drop _part- reference from example, introduce _split- entity #460

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[INFRA] Convert entity table to yaml #475

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ENH: provide an example for a suffix based on an _eeg.vhdr filename

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yarikoptic force-pushed the enh-glossary branch from 14fccdc to cd1c10e Compare May 22, 2020 16:00

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ENH: make NOT RECOMMENDED stronger (SHOULD NOT) for zero padding for …

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…uniqueness Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

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Merge remote-tracking branch 'origin/master' into enh-glossary

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* origin/master: [DOC] Auto-generate changelog entry for PR bids-standard#477 Also ignore users urls on github Quote regexp in command line [INFRA] linkchecker - ignore github pull and tree URLs

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Specify that suffix must be alphanumeric

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Please return leading . in extension bids-standard/pybids#618

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[DOC] Auto-generate changelog entry for PR #152

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Replace terms "modality_label" and "contrast_label" with "suffix" #571

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What to call modality directory vs the modality entity? #584

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Removing leading period from YAML extensions? #990

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[ENH] Allow for - (dash) (and/or +) in <label> #1165

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[ENH] Add Glossary of terms/abbreviations used in the specification #152

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yarikoptic commented May 22, 2020

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yarikoptic commented May 22, 2020

yarikoptic commented May 22, 2020

yarikoptic commented Feb 15, 2019 •

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effigies May 10, 2019 •

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tyarkoni commented May 11, 2019 •

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