[DO NOT MERGE] Backup bep032 work history #1
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otherwise "Electrophysiology" is too broad. Thanks @dorahermes for the note
I think this is what might have freaked out `schemacode_ci / windows-latest with Python 3 (pull_request) ` (windows only!) fails with a bunch of ``` 2024-04-19T19:13:44.2815607Z self = <encodings.cp1252.IncrementalDecoder object at 0x0000028D6A14D850> 2024-04-19T19:13:44.2818292Z input = b'---\nHED:\n name: HED\n display_name: HED Tag\n description: |\n Hierarchical Event Descriptor (HED) Tag.\n ...ed or ideal position along the z axis.\n anyOf:\n - type: number\n - type: string\n enum:\n - n/a\n' 2024-04-19T19:13:44.2820386Z final = True 2024-04-19T19:13:44.2820609Z 2024-04-19T19:13:44.2820821Z def decode(self, input, final=False): 2024-04-19T19:13:44.2821664Z > return codecs.charmap_decode(input,self.errors,decoding_table)[0] 2024-04-19T19:13:44.2823260Z E UnicodeDecodeError: 'charmap' codec can't decode byte 0x9d in position 2105: character maps to <undefined> 2024-04-19T19:13:44.2824229Z 2024-04-19T19:13:44.2824768Z C:\hostedtoolcache\windows\Python\3.12.3\x64\Lib\encodings\cp1252.py:23: UnicodeDecodeError ```
…es (bids-standard#1806) * RF: to have "microephys" (Microelectrode physiology) for modality and icephys and ecephys for suffixes and datatypes * Reflecting decision of having two separate datatypes under the Microelectrode Electrophysiology bids-standard#1800 (comment) Consensus reached during working group meeting on 2024-05-15: - modality = "Microelectrode Electrophysiology" - datatypes = "icephys" and "ecephys" - suffixes = "_icephys" and "_ecephys" * Adjust wording to Horea's recommendation * Various fixups and tune ups to wording from code review
…ctrode Electrophysiology
* test * MACROS___make_suffix_table * markdown * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * undoing changes to yaml files * adding chanell * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update src/modality-specific-files/microelectrode-electrophysiology.md Co-authored-by: Yaroslav Halchenko <[email protected]> * Update src/modality-specific-files/microelectrode-electrophysiology.md Co-authored-by: Yaroslav Halchenko <[email protected]> * Update src/modality-specific-files/microelectrode-electrophysiology.md Co-authored-by: Yaroslav Halchenko <[email protected]> * Update src/modality-specific-files/microelectrode-electrophysiology.md Co-authored-by: Yaroslav Halchenko <[email protected]> * Update src/modality-specific-files/microelectrode-electrophysiology.md Co-authored-by: Yaroslav Halchenko <[email protected]> * Update src/modality-specific-files/microelectrode-electrophysiology.md Co-authored-by: Yaroslav Halchenko <[email protected]> * Update src/modality-specific-files/microelectrode-electrophysiology.md Co-authored-by: Yaroslav Halchenko <[email protected]> * adding General ephys metadata * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Examples of real datasets * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Minor tuneups to formatting --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Yaroslav Halchenko <[email protected]>
* [FIX] Minor YAML formatting * [ENH] Added additional birthdate column for participants.tsv * [ENH] Added age_category, age_type and corresponding enums * [ENH] Added surgery_date column * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Reverted changes that better suit in a PR against master * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [ENH] Added tabular_data file and columns for _probes.tsv * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [ENH] Added tabular_data rules and columns for _electrodes.tsv * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [ENH] Added tabular_data rules for _electrodes.tsv * [ENH] Added tabular_data rules and columns for _channels.tsv * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [FIX] Fixed pre-commit errors * [ENH] Added additional ephys columns for events.tsv * [ENH] Added tabular data rules for events.tsv to include ephys related columns * [ENH] Added metadata entities for ephys setup metadata * [ENH] Created sidecar rule file for ephys metadata and added data origin and setup fields * Made schema changes to match microephys data type * Renamed rule files from ephys to microephys * Made schema changes to match microephys data type * [ENH] Added objects and rules for coordinate system sidecar file * [ENH] Added processing microephys metadata field in rules * [ENH] Added pharmaceuticals microephys metadata field in rules * [ENH] Added supplementary microephys metadata field and rules * [ENH] Added sample microephys metadata rules * [ENH] Added task microephys metadata rules * Fixed example language convention * Added microephys in schema rule modality * Corrected SampleThickness to SliceThickness * Add yaml document separator for microephys rules file It is optional, and adding does not solve anything but makes it consistent with the other files in the folder * BF: should be a dict, not a list of dicts --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Yaroslav Halchenko <[email protected]>
* origin/master: (288 commits) chore(deps): bump codecov/codecov-action from 4 to 5 (bids-standard#1989) chore: Bump schema post-dev version schema-0.11.3.post3 chore(ci): Fix pytest call for make_archive chore: Remove excess test data from bidsschematools installation directories (bids-standard#1985) feat(cli): Add tool for filename validation for use in pre-receive hooks (bids-standard#1986) rm COC (bids-standard#1979) chore: Bump schema post-dev version schema-0.11.3.post2 Update CONTRIBUTING.md (bids-standard#1978) fix(schema): Check SliceTiming length against SliceEncodingDirection fix(schema): Do not warn about missing events for task-noise fix(schema): Check for existence of stim_files in beh.tsv chore: Use GITHUB_REF(_NAME) correctly chore: Debug environment chore: Bump schema post-dev version schema-0.11.3.post1 chore: Output version, set correct env var chore: Update publish_schema to publish post-releases fix(schema): Include changes to schema that do not modify spec ... Conflicts: mkdocs.yml src/schema/objects/columns.yaml src/schema/objects/metadata.yaml src/schema/objects/modalities.yaml src/schema/objects/suffixes.yaml src/schema/rules/modalities.yaml
* origin/master: (26 commits) Update tools/schemacode/src/bidsschematools/types/namespace.py fail build on macro fails graceful error when failing to load invalid yml fix Update mkdocs.yml fix more seg Update src/modality-specific-files/electroencephalography.md fix channel, elec, sim recording fix key value and in-out fix tabular and seg reset fix internal links enh: Link all DICOM tags following standard pattern chore(links): Fix http -> https 301 redirects Update Release_Protocol.md (bids-standard#1997) schema-1.0.1-dev schema-1.0.0 [SCHEMA] Allow physio files for anat datatype (bids-standard#1961) FIX: Add 1.10.0 to known versions list (bids-standard#1994) ...
Co-authored-by: Peyman Najafi <[email protected]>
* cutting line lenghts * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * marking json examples * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * microephysChannels --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Ben Dichter <[email protected]>
* enhancement(units): Remove dimension_unit and add default mm for probe * cleanup: remove resolved comment * cleanup: remove resolved comment * cleanup(schema): mark hemisphere__probes for future unification with base hemispher column * cleanup: comments about unifying probes and electrodes column * fix(schema): use um² for microephys electrode size Microelectrodes require micrometer-scale measurements different from iEEG. Added size__microephys with um² units. * fix(schema): remove use of dimension_unit in microephys * cleanup: remove unused surgery_date column (moved as comment to PR bids-standard#1839) * fix(desc): include microephys for channel column in events * fix(typo): microeelectrode in events * refactor(schema): use base x/y/z columns with addendums for electrodes * change(units): remove unavailble dimension_unit reference and add um in accordance with ProbeInterface norms * fix(docs): add link to markdown for 2D coordinate systems * cleanup: remove resolved TODO comment by 6284d36 * cleanup(rule): remove unsused older check for coordystem file * future cleanup(schema): add a comment of a potential column desc unification * refactor(schema): use base unit column like iEEG for channels
Co-authored-by: Cody Baker <[email protected]>
Co-authored-by: Thomas Wachtler <[email protected]>
Co-authored-by: Thomas Wachtler <[email protected]>
Co-authored-by: Thomas Wachtler <[email protected]>
Co-authored-by: Thomas Wachtler <[email protected]>
…trophysiology documentation
…croelectrode electrophysiology documentation
Co-authored-by: Thomas Wachtler <[email protected]>
Co-authored-by: Thomas Wachtler <[email protected]>
Add electrode_name column to the extracellular electrophysiology channels.tsv example to show the mapping between channels and their corresponding electrodes.
…al Coordinates appendix to markdown
- Fix WaxholmSpace species from rat to mouse and update DOI reference - Remove RRID links from SwansonRat, CHARM, D99, and MarmosetBrainAtlas - Add DOI link for SwansonRat reference - Correct PaxinosRhesusMonkey author list (Toga AW -> Evrard, H)
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Legacy history for BEP032 work before it was squashed and submitted for community review in ??
Also viewable from original PR: bids-standard#1705