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[ENH] Encode mutually exclusive extensions in schema with sub-lists #1492

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[ENH] Encode mutually exclusive extensions in schema with sub-lists #1492

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3c72014
group extension
Remi-Gau May 18, 2023
13eabdd
add comment
Remi-Gau May 18, 2023
d3594e7
put all extension for data in list
Remi-Gau May 18, 2023
b0d5dd5
rename some funtions
Remi-Gau May 20, 2023
160b9c5
minor fixes
Remi-Gau May 20, 2023
1eb0f63
fx rendering
Remi-Gau May 20, 2023
bcf5ebc
attempt at fixing rules
Remi-Gau May 20, 2023
9708eb3
properly combine extensions
Remi-Gau May 20, 2023
e4b2922
add doc
Remi-Gau May 20, 2023
f28d3c2
import annotation for backward compatibility
Remi-Gau May 20, 2023
cd1da9d
add type hints
Remi-Gau May 20, 2023
0b05f28
Merge remote-tracking branch 'upstream/master' into one_extension
effigies May 26, 2023
341f7ae
RF: Fix extension list combination, remove some indirection
effigies May 29, 2023
d8e3ec6
update README
Remi-Gau May 29, 2023
e383905
TEST: Fix rendering tests
effigies May 31, 2023
a8bd1c3
RF: Convert extensions to lists-of-lists-of-strings
effigies May 30, 2023
586cd18
FIX: .mhd files are actually .raw.mhd
effigies May 31, 2023
d7e3f89
Merge remote-tracking branch 'upstream/master' into one_extension
effigies Jun 6, 2023
1fbb60b
MNT: Bump schema minor version to mark change to structure
effigies Jun 6, 2023
f693273
Merge branch 'master' into one_extension
effigies Jun 28, 2023
0d291c9
Merge branch 'master' into one_extension
effigies Jul 2, 2023
53c4fd3
Update src/schema/rules/files/raw/photo.yaml
Remi-Gau Jul 3, 2023
da67b35
remove digitizer
Remi-Gau Aug 10, 2023
6c092d8
fix some failing tests
Remi-Gau Aug 10, 2023
2ba8439
Merge branch 'master' into one_extension
effigies Aug 8, 2024
f297c30
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 8, 2024
3958ac0
fix: Adapt to extensions being list[list[str]]
effigies Aug 8, 2024
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4 changes: 2 additions & 2 deletions src/appendices/meg-file-formats.md
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Expand Up @@ -329,8 +329,8 @@ A guide for using macros can be found at
"sub-control01_ses-001_task-rest_run-01_meg": "",
"sub-control01_ses-001_task-rest_run-01_meg.json": "",
"sub-control01_ses-001_task-rest_run-01_channels.tsv": "",
"sub-control01_ses-001_task-rest[_acq-<label>]_run-01_markers.<mrk,sqd>": "",
"sub-control01_ses-001_task-rest_run-01_meg.<con,sqd>": "",
"sub-control01_ses-001_task-rest[_acq-<label>]_run-01_markers.<mrk|sqd>": "",
"sub-control01_ses-001_task-rest_run-01_meg.<con|sqd>": "",
},
},
},
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2 changes: 1 addition & 1 deletion src/modality-specific-files/magnetoencephalography.md
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Expand Up @@ -26,7 +26,7 @@ and a guide for using macros can be found at
{{ MACROS___make_filename_template(
"raw",
datatypes=["meg"],
suffixes=["meg", "markers", "events", "physio", "stim"])
suffixes=["meg", "markers", "events", "physio", "stim", "digitizer"])
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}}

Unprocessed MEG data MUST be stored in the native file format of the MEG
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4 changes: 4 additions & 0 deletions src/schema/objects/suffixes.yaml
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Expand Up @@ -551,6 +551,10 @@ defacemask:
description: |
A binary mask that was used to remove facial features from an anatomical MRI
image.
digitizer:
value: digitizer
display_name: Digitizer
description: Digitized positions of the head points.
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dseg:
value: dseg
display_name: Discrete Segmentation
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5 changes: 1 addition & 4 deletions src/schema/rules/files/common/core.yaml
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Expand Up @@ -9,10 +9,7 @@ README:
level: recommended
stem: README
extensions:
- ''
- .md
- .rst
- .txt
- ['', .md, .rst, .txt]
CHANGES:
level: optional
path: CHANGES
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12 changes: 4 additions & 8 deletions src/schema/rules/files/deriv/imaging.yaml
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Expand Up @@ -94,8 +94,7 @@ anat_parametric_discrete_segmentation:
density: optional
description: optional
extensions:
- .nii.gz
- .nii
- [.nii.gz, .nii]
- .json
- .tsv

Expand All @@ -110,8 +109,7 @@ anat_nonparametric_discrete_segmentation:
density: optional
description: optional
extensions:
- .nii.gz
- .nii
- [.nii.gz, .nii]
- .json
- .tsv

Expand Down Expand Up @@ -190,8 +188,7 @@ anat_parametic_discrete_surface:
suffixes:
- dseg
extensions:
- .label.gii
- .dlabel.nii
- [.label.gii, .dlabel.nii]
- .json
- .tsv
entities:
Expand All @@ -207,8 +204,7 @@ anat_nonparametic_discrete_surface:
suffixes:
- dseg
extensions:
- .label.gii
- .dlabel.nii
- [.label.gii, .dlabel.nii]
- .json
- .tsv
entities:
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27 changes: 9 additions & 18 deletions src/schema/rules/files/raw/anat.yaml
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Expand Up @@ -14,8 +14,7 @@ nonparametric:
- FLASH # deprecated
- PD # deprecated
extensions:
- .nii.gz
- .nii
- [.nii.gz, .nii]
- .json
datatypes:
- anat
Expand Down Expand Up @@ -48,8 +47,7 @@ parametric:
- S0map
- M0map
extensions:
- .nii.gz
- .nii
- [.nii.gz, .nii]
- .json
datatypes:
- anat
Expand All @@ -66,8 +64,7 @@ defacemask:
suffixes:
- defacemask
extensions:
- .nii.gz
- .nii
- [.nii.gz, .nii]
- .json
datatypes:
- anat
Expand All @@ -86,8 +83,7 @@ multiecho:
- MESE
- MEGRE
extensions:
- .nii.gz
- .nii
- [.nii.gz, .nii]
- .json
datatypes:
- anat
Expand All @@ -106,8 +102,7 @@ multiflip:
suffixes:
- VFA
extensions:
- .nii.gz
- .nii
- [.nii.gz, .nii]
- .json
datatypes:
- anat
Expand All @@ -127,8 +122,7 @@ multiinversion:
suffixes:
- IRT1
extensions:
- .nii.gz
- .nii
- [.nii.gz, .nii]
- .json
datatypes:
- anat
Expand All @@ -147,8 +141,7 @@ mp2rage:
suffixes:
- MP2RAGE
extensions:
- .nii.gz
- .nii
- [.nii.gz, .nii]
- .json
datatypes:
- anat
Expand All @@ -170,8 +163,7 @@ vfamt:
- MPM
- MTS
extensions:
- .nii.gz
- .nii
- [.nii.gz, .nii]
- .json
datatypes:
- anat
Expand All @@ -192,8 +184,7 @@ mtr:
suffixes:
- MTR
extensions:
- .nii.gz
- .nii
- [.nii.gz, .nii]
- .json
datatypes:
- anat
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6 changes: 2 additions & 4 deletions src/schema/rules/files/raw/dwi.yaml
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Expand Up @@ -3,8 +3,7 @@ dwi:
suffixes:
- dwi
extensions:
- .nii.gz
- .nii
- [.nii.gz, .nii]
- .json
- .bvec
- .bval
Expand All @@ -23,8 +22,7 @@ sbref:
suffixes:
- sbref
extensions:
- .nii.gz
- .nii
- [.nii.gz, .nii]
- .json
datatypes:
- dwi
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7 changes: 3 additions & 4 deletions src/schema/rules/files/raw/eeg.yaml
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Expand Up @@ -4,13 +4,12 @@ eeg:
- eeg
extensions:
- .json
- .edf
- [.bdf, .edf, .eeg, .set]
# .vhdr, .vmrk, .eeg must work as triplet
- .vhdr
- .vmrk
- .eeg
- .set
# .set file with an OPTIONAL .fdt
- .fdt
- .bdf
datatypes:
- eeg
entities:
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21 changes: 7 additions & 14 deletions src/schema/rules/files/raw/fmap.yaml
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Expand Up @@ -9,8 +9,7 @@ fieldmaps:
- magnitude
- fieldmap
extensions:
- .nii.gz
- .nii
- [.nii.gz, .nii]
- .json
datatypes:
- fmap
Expand All @@ -25,8 +24,7 @@ pepolar:
- epi
- m0scan
extensions:
- .nii.gz
- .nii
- [.nii.gz, .nii]
- .json
datatypes:
- fmap
Expand All @@ -42,8 +40,7 @@ TB1DAM:
suffixes:
- TB1DAM
extensions:
- .nii.gz
- .nii
- [.nii.gz, .nii]
- .json
datatypes:
- fmap
Expand All @@ -62,8 +59,7 @@ TB1EPI:
suffixes:
- TB1EPI
extensions:
- .nii.gz
- .nii
- [.nii.gz, .nii]
- .json
datatypes:
- fmap
Expand All @@ -86,8 +82,7 @@ RFFieldMaps:
- TB1RFM
- RB1COR
extensions:
- .nii.gz
- .nii
- [.nii.gz, .nii]
- .json
datatypes:
- fmap
Expand All @@ -107,8 +102,7 @@ TB1SRGE:
suffixes:
- TB1SRGE
extensions:
- .nii.gz
- .nii
- [.nii.gz, .nii]
- .json
datatypes:
- fmap
Expand All @@ -129,8 +123,7 @@ parametric:
- TB1map
- RB1map
extensions:
- .nii.gz
- .nii
- [.nii.gz, .nii]
- .json
datatypes:
- fmap
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6 changes: 2 additions & 4 deletions src/schema/rules/files/raw/func.yaml
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Expand Up @@ -5,8 +5,7 @@ func:
- cbv
- sbref
extensions:
- .nii.gz
- .nii
- [.nii.gz, .nii]
- .json
datatypes:
- func
Expand All @@ -26,8 +25,7 @@ phase:
suffixes:
- phase # deprecated
extensions:
- .nii.gz
- .nii
- [.nii.gz, .nii]
- .json
datatypes:
- func
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8 changes: 3 additions & 5 deletions src/schema/rules/files/raw/ieeg.yaml
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Expand Up @@ -3,15 +3,13 @@ ieeg:
suffixes:
- ieeg
extensions:
- .mefd/
- [.nwb, .edf, .mefd/, .eeg, .set]
- .json
- .edf
# .vhdr, .vmrk, .eeg must work as triplet
- .vhdr
- .eeg
- .vmrk
- .set
# .set file with an OPTIONAL .fdt
- .fdt
- .nwb
datatypes:
- ieeg
entities:
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40 changes: 25 additions & 15 deletions src/schema/rules/files/raw/meg.yaml
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Expand Up @@ -3,19 +3,31 @@ meg:
suffixes:
- meg
extensions:
- / # corresponds to BTi/4D data
- .ds/
- .json
- .fif
- .sqd
- .con
- .raw
- .ave
- .mrk
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.mrk seems to only exist for markers suffix

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yes, some context in this thread: #638 (comment) and in particular this reponse (i.e., why .mrk is only for the markers suffix, but .sqd can also be used for the brain data): #653 (comment)

- .kdf
- .mhd
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- .trg
# / corresponds to BTi/4D data
- [/, .ds/, .fif, .sqd, .con, .raw, .kdf]
- .ave # mentioned once in the appendix
# .raw and .raw.mhd work as a pair
- .raw.mhd
# .kdf with possible additional files .chn, .trg and _digitizer.txt (see other suffix group below)
- .chn
- .trg
datatypes:
- meg
entities:
subject: required
session: optional
task: required
acquisition: optional
run: optional
processing: optional
split: optional

headpoints:
suffixes:
- digitizer
extensions:
- .txt
datatypes:
- meg
entities:
Expand Down Expand Up @@ -61,8 +73,7 @@ headshape:
suffixes:
- headshape
extensions:
- .*
- .pos
- [.*, .pos]
datatypes:
- meg
entities:
Expand All @@ -74,8 +85,7 @@ markers:
suffixes:
- markers
extensions:
- .sqd
- .mrk
- [.sqd, .mrk]
datatypes:
- meg
entities:
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6 changes: 1 addition & 5 deletions src/schema/rules/files/raw/micr.yaml
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Expand Up @@ -19,11 +19,7 @@ microscopy:
- OCT
- SPIM
extensions:
- .ome.tif
- .ome.btf
- .ome.zarr/
- .png
- .tif
- [.ome.tif, .ome.btf, .ome.zarr/, .png, .tif]
- .json
datatypes:
- micr
Expand Down
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