[FIX] consistently refer to DICOM Tags throughout the specification#786
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sappelhoff merged 12 commits intobids-standard:masterfrom May 20, 2021
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[FIX] consistently refer to DICOM Tags throughout the specification#786sappelhoff merged 12 commits intobids-standard:masterfrom
sappelhoff merged 12 commits intobids-standard:masterfrom
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tsalo
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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)
effigies
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@sappelhoff - while it doesn't matter from a doc perspective, just a note that dicom tags are hexadecimal so |
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
effigies
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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. |
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* [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 <markiewicz@stanford.edu> * 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 <markiewicz@stanford.edu> * 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 <markiewicz@stanford.edu> * 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 <stefan.appelhoff@mailbox.org> * Generalize SoftwareFilters example. * Distinguish AnatomicalLandmarkCoordinates definitions. * Rename fmapEchoTime to match new format. * Apply suggestions from code review Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org> * Apply suggestions from code review Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org> * 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 <stefan.appelhoff@mailbox.org> * 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 <stefan.appelhoff@mailbox.org> * Update src/schema/metadata/RepetitionTimeExcitation.yaml Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org> * Add DoseCalibrationFactor. * Update ScanDate definition and deprecate it. * Remove hardcoded tables. * Remove unused links. * Update tools/schemacode/schema.py Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu> Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu> Co-authored-by: Remi Gau <remi_gau@hotmail.com> Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org> Co-authored-by: mnoergaard <martin.noergaard@nru.dk>
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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