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[FIX] consistently refer to DICOM Tags throughout the specification #786

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merged 12 commits into from
May 20, 2021
Merged

[FIX] consistently refer to DICOM Tags throughout the specification #786

merged 12 commits into from
May 20, 2021

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Hboni
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@Hboni Hboni commented Apr 23, 2021

Only some changes for Dicom tag representation to be consistent across the page and as used in MRI.
Also, remove what I think is duplicate in a figure caption

tsalo added a commit that referenced this pull request Apr 26, 2021
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Fix typos in PET metadata
4d6cd67 
From #786.
@Hboni Hboni requested a review from chrisgorgo as a code owner May 14, 2021 09:39
@sappelhoff sappelhoff changed the title [FIX] typos in PET Dicom tags [FIX] consistently refer to DICOM Tags throughout the specification May 14, 2021
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sappelhoff approved these changes May 14, 2021
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Thanks for seeing this and fixing a bunch of these inconsistencies @Hboni.

I took your start and made a pass through the whole spec, so that we always use DICOM Tag \d+, \d+

Also thanks for removing that duplication in the caption!

PS: You made this PR from your master branch. Just for next time, I recommend that you make a separate branch off your (up to date) master branch to submit changes/proposals --> that can avoid some git difficulties that we luckily didn't run into here (so far)

@sappelhoff sappelhoff requested a review from tsalo May 14, 2021 09:45
@sappelhoff sappelhoff mentioned this pull request May 14, 2021
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@sappelhoff sappelhoff added the formatting Aesthetics and formatting of the spec label May 14, 2021
@sappelhoff sappelhoff requested a review from effigies May 19, 2021 12:42
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satra commented May 19, 2021

so that we always use DICOM Tag \d+, \d+

@sappelhoff - while it doesn't matter from a doc perspective, just a note that dicom tags are hexadecimal so [a-e\d]{4} or 0x[a-e\d]{4} if you want to make it explicit (in a programming sense).

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Thanks both. To be clear: I don't know how we would want DICOM tags to be formatted in the spec. I am simply completing/fixing up @Hboni's start to make the formatting consistent based on which convention was initially used in the spec. Prior to PET, ASL, qMRI adding some more tags.

@sappelhoff sappelhoff merged commit f7fd3c2 into bids-standard:master May 20, 2021
bids-maintenance added a commit that referenced this pull request May 20, 2021
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[DOC] Auto-generate changelog entry for PR #786
93c7951
tsalo added a commit that referenced this pull request Jul 13, 2021
@tsalo @effigies
@Remi-Gau @sappelhoff @mnoergaard
[SCHEMA] Add metadata term files (#774)
5de7cfc 
* [SCHEMA] Add metadata term files (#762)

* Draft a handful of metadata term files.

* Add example with specific possible values.

* Match the validator schemas better.

* Fix formatting.

* Fix formatting again!

* Draft semi-functional rendering functions.

* Use unit abbreviations.

* Add more fields.

* Get macro working.

* Add terms from first table.

* Add AnatomicalLandmarkCoordinateSystem.

* fMRI task information table.

* More terms.

* More terms.

* More terms.

* EchoTime and FlipAngle

* Add tables.

* More tables.

* More terms.

* More terms.

* More terms.

* Fix spacing.

* Clean things up.

* More terms.

* More terms!

* More terms.

* Some iEEG terms.

* More iEEG terms.

* Add ASL labeling terms.

* Next batch.

* More terms.

* More terms.

* More terms.

* Fix mistakes.

* Last terms.

* Reference yamls.

* Fix mistakes.

* Change format of coordinate system files.

* Use degree in associated files.

* Some of the missing terms.

* A few more terms.

* Fix typos.

* More terms.

* More terms.

* More terms.

* More terms.

* More terms.

* More terms.

* Last terms.

* Fix link.

* Fix internal links.

* Fix links for real.

* Derivative terms.

* Fix up code link.

* Use backslashes for continued strings.

* Replace $ref with file contents.

Also support plural datatype strings and all manner of newlines in descriptions.

* Fix genetics.

* Describe the structure of metadata YAML files.

* Make metadatatype function recursive.

* Improve search function.

* Start adding PET fields.

* Add some fields.

* More terms.

* More terms.

* More terms.

* Fix mistakes.

* More terms.

* Replace InstitutionDepartmentName with existing InstitutionalDepartmentName.

* More terms.

* More terms.

* More terms.

* More terms.

* More terms.

* More terms.

* More terms.

* Last terms.

* Add unit format for strings.

Unused for now but could be useful later.

* Add dataset_relative and participant_relative string formats.

* Update READMEs.

* Fix formats in README.

* Support table-specific metadata description extensions.

* Employ description extensions with IntendedFor.

* Remove explicit defaults from YAML files.

* Replace Minimum with minimum.

* Replace inclusiveMaximum with maximum.

* Replace implicit links with explicit ones.

* Rename key_name to name.

* Rename "Unit" to "Units"

* Improve make_metadata_table docstring.

* Start addressing inconsistencies between rendered and hardcoded tables.

* Fix typos in PET metadata

From #786.

* Add metadata fields from qMRI appendix.

* Fix.

* Address duplicate datatypes.

Should address the "string or string or string or string" issue.

* Wrap example strings in code.

* Use enum for n/a instead of pattern.

It's easier to identify as a special case.

* Replace "string" with "n/a" when appropriate.

* Address some inconsistencies.

* Take a crack as SpatialReference.

The type is complicated, but I _think_ I've got it figured out.

* Apply suggestions from code review

Thanks @effigies!

Co-authored-by: Chris Markiewicz <[email protected]>

* Update tools/schemacode/schema.py

* search_structure --> dereference_yaml

* Use faster loading approach.

* Fix deprecation link.

* Apply suggestions from code review

Co-authored-by: Chris Markiewicz <[email protected]>

* Update 01-magnetic-resonance-imaging-data.md

* Add B0FieldIdentifier and B0FieldSource.

* Revert type changes and add TODOs to check them.

* Update tools/schemacode/schema.py

* Replace remaining relative links.

* Apply suggestions from code review

Co-authored-by: Chris Markiewicz <[email protected]>

* Add new coordinate systems from #775.

* Grab hack from #781 (which wasn't merged).

* Create HED.yaml

* boldify table headers

* add device info metadata

* fix table fences

* fix cell padding

* fix cell padding

this is getting old VERY quickly

* Fix up DICOM tags in metadata.

* Leverage "name" field for section-specific metadata definitions.

* composite instances --> measurements

Changes from #813.

* Fix name of HED field.

* Fix string formatting in coordinate system fields.

* Move "preferably same as" to section-specific text.

For #774 (comment)

* Standardize DICOM Tag format.

Still need to move the references out of the generic definitions.

* Move mentions of DICOM Tags out of definitions.

Only for fields that *also* appear in modalities that *don't* use DICOM.

* Apply suggestions from code review

Co-authored-by: Stefan Appelhoff <[email protected]>

* Generalize SoftwareFilters example.

* Distinguish AnatomicalLandmarkCoordinates definitions.

* Rename fmapEchoTime to match new format.

* Apply suggestions from code review

Co-authored-by: Stefan Appelhoff <[email protected]>

* Apply suggestions from code review

Co-authored-by: Stefan Appelhoff <[email protected]>

* Address review.

* Fix example manufacturer names.

* TEMPORARY: fix osipi URL (revert when osipi.org is back)

* Fix regex for identifying macros.

* Partially address review.

* Do not assume minItems is 1 for array terms.

* composite instances --> measurements (again)

* Update src/schema/metadata/MagneticFieldStrength.yaml

Co-authored-by: Stefan Appelhoff <[email protected]>

* Update description to PharmaceuticalDoseTime

#774 (comment)

* Update 09-positron-emission-tomography.md

* fix table pipe alignment

* add pharmaceuticaldosetime fix to schema

includes a bugfix to convert "should" (not casing, this was not intended
as a SHOULD) to a MUST.

* fix str examples

* Apply suggestions from code review

Co-authored-by: Stefan Appelhoff <[email protected]>

* Update src/schema/metadata/RepetitionTimeExcitation.yaml

Co-authored-by: Stefan Appelhoff <[email protected]>

* Add DoseCalibrationFactor.

* Update ScanDate definition and deprecate it.

* Remove hardcoded tables.

* Remove unused links.

* Update tools/schemacode/schema.py

Co-authored-by: Chris Markiewicz <[email protected]>

Co-authored-by: Chris Markiewicz <[email protected]>
Co-authored-by: Remi Gau <[email protected]>
Co-authored-by: Stefan Appelhoff <[email protected]>
Co-authored-by: mnoergaard <[email protected]>
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@effigies effigies effigies approved these changes

@sappelhoff sappelhoff sappelhoff approved these changes

@chrisgorgo chrisgorgo Awaiting requested review from chrisgorgo

@tsalo tsalo Awaiting requested review from tsalo

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@Hboni @satra @sappelhoff @effigies