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[FIX] Improve setRun() functionality when sequences contain part and …
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…echo entities
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Dan Levitas committed Nov 3, 2023
1 parent 4e75e24 commit e2a4a91
Showing 1 changed file with 166 additions and 62 deletions.
228 changes: 166 additions & 62 deletions ui/src/libUnsafe.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -220,7 +220,6 @@ export function fmapQA($root:IEzbids) {
https://bids-specification.readthedocs.io/en/stable/99-appendices/11-qmri.html
*/

let fmapM0scan = section.filter(o=>o._type === "fmap/m0scan") //pair
let fmapTB1DAM = section.filter(o=>o._type === "fmap/TB1DAM") //pair
let fmapTB1EPI = section.filter(o=>o._type === "fmap/TB1EPI") //pair
let fmapTB1AFI = section.filter(o=>o._type === "fmap/TB1AFI") //pair
Expand Down Expand Up @@ -295,7 +294,7 @@ export function fmapQA($root:IEzbids) {
}

// several of the quantitative MRI field maps come in pairs, so validate them the same way
for (const fmap of [fmapM0scan, fmapTB1EPI, fmapTB1AFI, fmapTB1TFL, fmapTB1RFM, fmapRB1COR, fmapTB1SRGE, fmapTB1DAM]) {
for (const fmap of [fmapTB1EPI, fmapTB1AFI, fmapTB1TFL, fmapTB1RFM, fmapRB1COR, fmapTB1SRGE, fmapTB1DAM]) {
if (fmap.length) {
if (fmap.length < 2) {
fmap.forEach((o:IObject) => {
Expand Down Expand Up @@ -335,7 +334,9 @@ export function setRun($root:IEzbids) {
sesGroup.objects.forEach((obj:IObject) => {

// leave two entity labels out for now: part and run. The part entity could have a pairing (mag/phase or real/imag), and we're interested in the run entity
let targetEntities = Object.fromEntries(Object.entries(obj._entities).filter(([key])=>key !== "part" && key !== "run" && key !== "echo"))

let targetEntities = Object.fromEntries(Object.entries(obj._entities).filter(([key])=>key !== "part" && key !== "run" && key !== "echo")) // REFERENCE
// let targetEntities = Object.fromEntries(Object.entries(obj._entities).filter(([key])=>key !== "part" && key !== "run"))

let initialGrouping = sesGroup.objects.filter(e=>e._type !== "exclude" &&
!e._exclude &&
Expand All @@ -359,42 +360,82 @@ export function setRun($root:IEzbids) {
if (setRun) {
let run = 1
initialGrouping.forEach((o:IObject) => {
if (o._entities.part && ["", "mag", "real"].includes(o._entities.part)) {
o._entities.run = run.toString()
o.entities.run = o._entities.run
run++
} else if (o._entities.part && !["", "mag", "real"].includes(o._entities.part)) {
if (o._entities.part === "phase") {
let correspondingFuncMag = initialGrouping.filter(e=>e._entities.part === "mag" &&
((e.idx === o.idx - 1 && e._type === "func/bold") || (e.idx === o.idx - 2 && e._type === "func/bold"))
)

if (!correspondingFuncMag.length) {
o._exclude = true
o.exclude = true
o.validationWarnings = ["There is no corresponding func/bold (part-mag) sequence, therefore this sequence will be excluded from BIDS conversion"]
} else {
o._entities.run = correspondingFuncMag[0]._entities.run
if (o._entities.part) {
if (["mag", "real"].includes(o._entities.part)) {
if (o._entities.echo) {
if (o._entities.echo === "1") {
o._entities.run = run.toString()
o.entities.run = o._entities.run
run++
} else { // echo > 1
o._entities.run = (run-1).toString()
o.entities.run = o._entities.run
}
} else { // no echo entity
o._entities.run = run.toString()
o.entities.run = o._entities.run
run++
}
} else if (["phase", "imag"].includes(o._entities.part)) { // part entity is "phase" or "imag"

let corresponding_part = ""
if (o._entities.part === "phase") {
corresponding_part = "mag"
} else {
corresponding_part = "real"
}

if (o._entities.echo) {
let correspondingFuncMag = initialGrouping.filter(e=>e._entities.part === corresponding_part &&
e._type === o._type &&
e._entities.echo === o._entities.echo
)

if (!correspondingFuncMag.length) {
o._exclude = true
o.exclude = true
o.validationWarnings = ["There is no corresponding "+o._type+" (part-"+corresponding_part+", echo-"+o._entities.echo+") sequence, therefore this sequence will be excluded from BIDS conversion"]
} else {
let correspondingFuncMagFinal = correspondingFuncMag.filter(e=>e.ModifiedSeriesNumber === (Number(o.ModifiedSeriesNumber) - 1).toString())
if (!correspondingFuncMagFinal.length) {
o._exclude = true
o.exclude = true
o.validationWarnings = ["There is no corresponding "+o._type+" (part-part-"+corresponding_part+") sequence, therefore this sequence will be excluded from BIDS conversion"]
} else {
o._entities.run = correspondingFuncMagFinal[0]._entities.run
o.entities.run = o._entities.run
}
}
} else { // no echo entity
let correspondingFuncMag = initialGrouping.filter(e=>e._entities.part === corresponding_part &&
((e.idx === o.idx - 1 && e._type === o._type) || (e.idx === o.idx - 2 && e._type === o._type))
)

if (!correspondingFuncMag.length) {
o._exclude = true
o.exclude = true
o.validationWarnings = ["There is no corresponding "+o._type+" (part-part-"+corresponding_part+") sequence, therefore this sequence will be excluded from BIDS conversion"]
} else {
o._entities.run = correspondingFuncMag[0]._entities.run
o.entities.run = o._entities.run
}
}
} else if (o._entities.part === "imag") {
let correspondingFuncReal = initialGrouping.filter(e=>e._entities.part === "real" &&
((e.idx === o.idx - 1 && e._type === "func/bold") || (e.idx === o.idx - 2 && e._type === "func/bold"))
)

if (!correspondingFuncReal.length) {
o._exclude = true
o.exclude = true
o.validationWarnings = ["There is no corresponding func/bold (part-real) sequence, therefore this sequence will be excluded from BIDS conversion"]
}
} else { // no part entity
if (o._entities.echo) {
if (o._entities.echo === "1") {
o._entities.run = run.toString()
o.entities.run = o._entities.run
run++
} else {
o._entities.run = correspondingFuncReal[0]._entities.run
o._entities.run = (run-1).toString()
o.entities.run = o._entities.run
}
} else {
o._entities.run = run.toString()
o.entities.run = o._entities.run
run++
}
} else {
o._entities.run = run.toString()
o.entities.run = o._entities.run
run++
}
})
} else {
Expand All @@ -409,6 +450,92 @@ export function setRun($root:IEzbids) {
})
}

// export function setRun($root:IEzbids) { // REFERENCE
// // Set run entity label for all objects, if appropriate.
// // Applied on the Dataset Review page.

// // Loop through subjects
// $root._organized.forEach((subGroup:OrganizedSubject) => {
// // Loop through sessions
// subGroup.sess.forEach((sesGroup:OrganizedSession) => {
// sesGroup.objects.forEach((obj:IObject) => {

// // leave two entity labels out for now: part and run. The part entity could have a pairing (mag/phase or real/imag), and we're interested in the run entity
// let targetEntities = Object.fromEntries(Object.entries(obj._entities).filter(([key])=>key !== "part" && key !== "run" && key !== "echo"))

// let initialGrouping = sesGroup.objects.filter(e=>e._type !== "exclude" &&
// !e._exclude &&
// e._type === obj._type &&
// e._type !== "func/events" && // let users specify the run number for func/events files
// deepEqual(Object.fromEntries(Object.entries(e._entities).filter(([key])=>key !== "part" && key !== "run" && key !== "echo")), targetEntities)
// )
// // console.log(initialGrouping)

// if (initialGrouping.length) {
// // Sort this new array by idx (i.e. order in which the sequences were collected in the scanner)
// initialGrouping.sort((a, b) => a.idx - b.idx)

// let setRun = false
// if (initialGrouping.length > 1) {
// setRun = true
// // } else if (initialGrouping.length === 1 && (initialGrouping[0]._type.includes("anat") || initialGrouping[0]._type.includes("func"))) { // might need to add conditional for not having func/events
// } else if (initialGrouping.length === 1 && (initialGrouping[0]._type.includes("func"))) { // might need to add conditional for not having func/events
// setRun = true
// }

// if (setRun) {
// let run = 1
// initialGrouping.forEach((o:IObject) => {
// if (o._entities.part && ["", "mag", "real"].includes(o._entities.part)) {
// o._entities.run = run.toString()
// o.entities.run = o._entities.run
// run++
// } else if (o._entities.part && !["", "mag", "real"].includes(o._entities.part)) {
// if (o._entities.part === "phase") {
// let correspondingFuncMag = initialGrouping.filter(e=>e._entities.part === "mag" &&
// ((e.idx === o.idx - 1 && e._type === "func/bold") || (e.idx === o.idx - 2 && e._type === "func/bold"))
// )

// if (!correspondingFuncMag.length) {
// o._exclude = true
// o.exclude = true
// o.validationWarnings = ["There is no corresponding func/bold (part-mag) sequence, therefore this sequence will be excluded from BIDS conversion"]
// } else {
// o._entities.run = correspondingFuncMag[0]._entities.run
// o.entities.run = o._entities.run
// }
// } else if (o._entities.part === "imag") {
// let correspondingFuncReal = initialGrouping.filter(e=>e._entities.part === "real" &&
// ((e.idx === o.idx - 1 && e._type === "func/bold") || (e.idx === o.idx - 2 && e._type === "func/bold"))
// )

// if (!correspondingFuncReal.length) {
// o._exclude = true
// o.exclude = true
// o.validationWarnings = ["There is no corresponding func/bold (part-real) sequence, therefore this sequence will be excluded from BIDS conversion"]
// } else {
// o._entities.run = correspondingFuncReal[0]._entities.run
// o.entities.run = o._entities.run
// }
// }
// } else {
// o._entities.run = run.toString()
// o.entities.run = o._entities.run
// run++
// }
// })
// } else {
// initialGrouping.forEach((o:IObject) => {
// o._entities.run = ""
// o.entities.run = o._entities.run
// })
// }
// }
// })
// })
// })
// }

export function setIntendedFor($root:IEzbids) {
// Apply fmap intendedFor mapping, based on user specifications on Series page.

Expand Down Expand Up @@ -439,31 +566,6 @@ export function setIntendedFor($root:IEzbids) {
});
}
}
// if (obj._type.startsWith("fmap/") || obj._type === "perf/m0scan") {
// if (!obj.IntendedFor) {
// Object.assign(obj, {IntendedFor: []})
// }

// let correspindingSeriesIntendedFor = $root.series[obj.series_idx].IntendedFor
// if (correspindingSeriesIntendedFor !== undefined && correspindingSeriesIntendedFor !== null) {
// correspindingSeriesIntendedFor.forEach((i:number) => {
// let IntendedForIDs = section.filter(o=>o.series_idx === i && o._type !== "func/events").map(o=>o.idx)
// if (obj.IntendedFor !== undefined) {
// IntendedForIDs.forEach((IntendedForID:number) => {
// if (!obj.IntendedFor?.includes(IntendedForID)) {
// obj.IntendedFor = obj.IntendedFor?.concat(IntendedForIDs)
// }

// let IntendedForObj = sesGroup.objects.filter(e=>e.idx === IntendedForID)[0]
// console.log(IntendedForObj)
// if (IntendedForObj._exclude || IntendedForObj._type === "exclude") {
// obj.IntendedFor = obj.IntendedFor?.filter(e=>e === IntendedForID)
// }
// })
// }
// });
// }
// }

// check B0FieldIdentifier and B0FieldSource information
if (obj._type && !obj._type.includes('exclude') && !obj._type.includes('events')) {
Expand Down Expand Up @@ -658,8 +760,10 @@ export function validateEntities(level:string, info:any) {
}
for (const i of values) {
if (i !== "imag") {
if (entities[k] === i && level === "Series" && !info.ImageType.includes(i.toUpperCase())) {
info.validationWarnings.push(`ezBIDS detects that this image is not part-${i}. Please verify before continuing`)
if (i !== "mag") {
if (entities[k] === i && level === "Series" && !info.ImageType.includes(i.toUpperCase())) {
info.validationWarnings.push(`ezBIDS detects that this image is not part-${i}. Please verify before continuing`)
}
}
} else {
if (entities[k] === i && level === "Series" && !info.ImageType.includes("IMAGINARY")) {
Expand Down Expand Up @@ -1245,7 +1349,7 @@ export function fileLogicLink($root:IEzbids, o:IObject) {
Any phase data (part-phase) is linked to the magnitude. If part entity is specified, make sure it's
properly linked and has same entities (except for part) and exclusion criteria.
*/
if(o._entities.part && !["", "mag", "real"].includes(o._entities.part)) {
if(o._entities.part && !["mag", "real"].includes(o._entities.part)) {
let correspondingFuncMag = $root.objects.filter((object:IObject)=>object._type === o._type &&
object._entities.part === "mag" &&
((object.idx === o.idx - 1 && object._type === "func/bold") || (object.idx === o.idx - 2 && object._type === "func/bold"))
Expand All @@ -1255,7 +1359,7 @@ export function fileLogicLink($root:IEzbids, o:IObject) {
correspondingFuncMag.forEach((boldMag:IObject)=>{
// o.analysisResults.section_id = boldObj.analysisResults.section_id
for(let k in boldMag._entities) {
if (k !== "part") {
if (k !== "part" && k !== "echo") {
if (boldMag._entities[k] !== "") {
o._entities[k] = boldMag._entities[k]
} else {
Expand Down

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