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[ENH] add support for qMRI json in top dir #1546

Merged
merged 13 commits into from
Feb 27, 2023
Merged

[ENH] add support for qMRI json in top dir #1546

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84b4410
add basic rule for mp2rage json in top dir
Remi-Gau Oct 10, 2022
55f4836
add ce entity in those allowed in root dir for anat
Remi-Gau Oct 21, 2022
7396685
add MTR
Remi-Gau Oct 21, 2022
1e9c9ec
add MTS
Remi-Gau Oct 21, 2022
a86d7ef
add MPM
Remi-Gau Oct 21, 2022
2657364
add IRT1
Remi-Gau Oct 21, 2022
6fb5f03
add MESE and MEGRE
Remi-Gau Oct 21, 2022
1e43b97
add VFA
Remi-Gau Oct 21, 2022
ce3d943
add qmri fmap
Remi-Gau Oct 21, 2022
a82055f
test on bids example and update
Remi-Gau Jan 2, 2023
f684ba2
make all entities optional at top level for new qmri buddies
rwblair Feb 22, 2023
957d7ee
make mprage2 top level entity optional
rwblair Feb 23, 2023
7e8e846
Merge branch 'master' into qmri_top
Remi-Gau Feb 23, 2023
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68 changes: 66 additions & 2 deletions bids-validator/bids_validator/rules/top_level_rules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,13 @@
"phase1\\.json",
"phase2\\.json",
"fieldmap\\.json",
"TB1DAM\\.json",
"TB1EPI\\.json",
"TB1AFI\\.json",
"TB1TFL\\.json",
"TB1RFM\\.json",
"TB1SRGE\\.json",
"RB1COR\\.json",
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"events\\.json",
"scans\\.json",
"samples\\.json",
Expand Down Expand Up @@ -59,7 +66,7 @@
},

"anat_top": {
"regexp": "^[\\/\\\\](?:ses-[a-zA-Z0-9]+_)?(?:acq-[a-zA-Z0-9]+_)?(?:rec-[a-zA-Z0-9]+_)?(?:run-[0-9]+_)?(@@@_anat_suffixes_@@@)\\.json$",
"regexp": "^[\\/\\\\](?:ses-[a-zA-Z0-9]+_)?(?:acq-[a-zA-Z0-9]+_)?(?:ce-[a-zA-Z0-9]+_)?(?:rec-[a-zA-Z0-9]+_)?(?:run-[0-9]+_)?(@@@_anat_suffixes_@@@)\\.json$",
"tokens": {
"@@@_anat_suffixes_@@@": [
"T1w",
Expand All @@ -77,11 +84,68 @@
"T2star",
"FLASH",
"PDmap",
"photo"
"photo",
"VFA",
"MEGRE",
"MESE",
"IRT1",
"MPM",
"MTS",
"MTR",
"MP2RAGE"
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]
}
},

"VFA_top": {
"regexp": "^[\\/\\\\](?:ses-[a-zA-Z0-9]+_)?(?:acq-[a-zA-Z0-9]+_)?(?:ce-[a-zA-Z0-9]+_)?(?:rec-[a-zA-Z0-9]+_)?(?:run-[0-9]+_)?(?:echo-[0-9]+_)?flip-[0-9]+_(?:part-(mag|phase|real|imag)_)?(@@@_mese_megre_suffixes_@@@)\\.json$",
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"tokens": {
"@@@_mese_megre_suffixes_@@@": ["VFA"]
}
},

"megre_mese_top": {
"regexp": "^[\\/\\\\](?:ses-[a-zA-Z0-9]+_)?(?:acq-[a-zA-Z0-9]+_)?(?:ce-[a-zA-Z0-9]+_)?(?:rec-[a-zA-Z0-9]+_)?(?:run-[0-9]+_)?echo-[0-9]+_(?:part-(mag|phase|real|imag)_)?(@@@_mese_megre_suffixes_@@@)\\.json$",
"tokens": {
"@@@_mese_megre_suffixes_@@@": ["MEGRE", "MESE"]
}
},

"irt1_top": {
"regexp": "^[\\/\\\\](?:ses-[a-zA-Z0-9]+_)?(?:acq-[a-zA-Z0-9]+_)?(?:ce-[a-zA-Z0-9]+_)?(?:rec-[a-zA-Z0-9]+_)?(?:run-[0-9]+_)?inv-[0-9]+_(?:part-(mag|phase|real|imag)_)?(@@@_irt1_suffixes_@@@)\\.json$",
"tokens": {
"@@@_irt1_suffixes_@@@": ["IRT1"]
}
},

"mpm_top": {
"regexp": "^[\\/\\\\](?:ses-[a-zA-Z0-9]+_)?(?:acq-[a-zA-Z0-9]+_)?(?:ce-[a-zA-Z0-9]+_)?(?:rec-[a-zA-Z0-9]+_)?(?:run-[0-9]+_)?(?:echo-[0-9]+_)?(?:flip-[0-9]+_)?mt-(on|off)_(?:part-(mag|phase|real|imag)_)?(@@@_mpm_suffixes_@@@)\\.json$",
"tokens": {
"@@@_mpm_suffixes_@@@": ["MPM"]
}
},

"mts_top": {
"regexp": "^[\\/\\\\](?:ses-[a-zA-Z0-9]+_)?(?:acq-[a-zA-Z0-9]+_)?(?:ce-[a-zA-Z0-9]+_)?(?:rec-[a-zA-Z0-9]+_)?(?:run-[0-9]+_)?(?:echo-[0-9]+_)?flip-[0-9]+_mt-(on|off)_(?:part-(mag|phase|real|imag)_)?(@@@_mts_suffixes_@@@)\\.json$",
"tokens": {
"@@@_mts_suffixes_@@@": ["MTS"]
}
},

"mtr_top": {
"regexp": "^[\\/\\\\](?:ses-[a-zA-Z0-9]+_)?(?:acq-[a-zA-Z0-9]+_)?(?:ce-[a-zA-Z0-9]+_)?(?:rec-[a-zA-Z0-9]+_)?(?:run-[0-9]+_)?mt-(on|off)_(?:part-(mag|phase|real|imag)_)?(@@@_mtr_suffixes_@@@)\\.json$",
"tokens": {
"@@@_mtr_suffixes_@@@": ["MTR"]
}
},

"mp2rage_top": {
"regexp": "^[\\/\\\\](?:ses-[a-zA-Z0-9]+_)?(?:acq-[a-zA-Z0-9]+_)?(?:ce-[a-zA-Z0-9]+_)?(?:rec-[a-zA-Z0-9]+_)?(?:run-[0-9]+_)?(?:echo-[0-9]+_)?(?:flip-[0-9]+_)?(?:inv-[0-9]+_)(?:part-(mag|phase|real|imag)_)?(@@@_mp2rage_suffixes_@@@)\\.json$",
"tokens": {
"@@@_mp2rage_suffixes_@@@": ["MP2RAGE"]
}
},

"dwi_top": {
"regexp": "^[\\/\\\\](?:ses-[a-zA-Z0-9]+_)?(?:acq-[a-zA-Z0-9]+_)?(?:rec-[a-zA-Z0-9]+_)?(?:run-[0-9]+_)?(dwi\\.(?:@@@_dwi_top_ext_@@@)|sbref\\.json)$",
"tokens": {
Expand Down
21 changes: 21 additions & 0 deletions bids-validator/utils/type.js
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Original file line number Diff line number Diff line change
Expand Up @@ -84,6 +84,13 @@ const rootTop = buildRegExp(top_level_rules.root_top)
const funcTop = buildRegExp(top_level_rules.func_top)
const aslTop = buildRegExp(top_level_rules.asl_top)
const anatTop = buildRegExp(top_level_rules.anat_top)
const vfaTop = buildRegExp(top_level_rules.VFA_top)
const megreTop = buildRegExp(top_level_rules.megre_mese_top)
const irt1Top = buildRegExp(top_level_rules.irt1_top)
const mpmTop = buildRegExp(top_level_rules.mpm_top)
const mtsTop = buildRegExp(top_level_rules.mts_top)
const mtrTop = buildRegExp(top_level_rules.mtr_top)
const mp2rageTop = buildRegExp(top_level_rules.mp2rage_top)
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const dwiTop = buildRegExp(top_level_rules.dwi_top)
const eegTop = buildRegExp(top_level_rules.eeg_top)
const ieegTop = buildRegExp(top_level_rules.ieeg_top)
Expand Down Expand Up @@ -141,6 +148,13 @@ export default {
aslTop.test(path) ||
dwiTop.test(path) ||
anatTop.test(path) ||
vfaTop.test(path) ||
megreTop.test(path) ||
irt1Top.test(path) ||
mpmTop.test(path) ||
mtsTop.test(path) ||
mtrTop.test(path) ||
mp2rageTop.test(path) ||
multiDirFieldmap.test(path) ||
otherTopFiles.test(path) ||
megTop.test(path) ||
Expand All @@ -157,6 +171,13 @@ export default {
aslTop.test(path) ||
dwiTop.test(path) ||
anatTop.test(path) ||
vfaTop.test(path) ||
megreTop.test(path) ||
irt1Top.test(path) ||
mpmTop.test(path) ||
mtsTop.test(path) ||
mtrTop.test(path) ||
mp2rageTop.test(path) ||
multiDirFieldmap.test(path) ||
otherTopFiles.test(path) ||
megTop.test(path) ||
Expand Down