diff --git a/deploy/atlas/index.js b/deploy/atlas/index.js
index ef4c1317da1ac775fc35a7faf18d261bc63ffd91..8d0e1a564740562d9da7ece8da83f1ccf4fc953e 100644
--- a/deploy/atlas/index.js
+++ b/deploy/atlas/index.js
@@ -27,20 +27,44 @@ router.get('/ready', (req, res) => {
}
})
+router.get('/preview', (req, res) => {
+ res.status(501).end()
+})
+
router.get('/:atlasId', async (req, res) => {
const { atlasId } = req.params
- const { templateSpaces, ...rest } = await getAtlasById(atlasId)
+ const { templateSpaces, parcellations, ...rest } = await getAtlasById(atlasId)
+
+ const searchParam = new url.URLSearchParams()
+ searchParam.set('id', atlasId)
+ const lastPathPreview = `preview?${searchParam.toString()}`
return res.status(200).json({
...rest,
+ previewUrl: res.locals.routePathname
+ ? url.resolve(`${res.locals.routePathname}/`, lastPathPreview)
+ : lastPathPreview,
+ parcellations: parcellations.map(p => {
+ const spSearchParam = new url.URLSearchParams()
+ spSearchParam.set('id', p['@id'])
+ const parcellationPreview = `preview?${spSearchParam.toString()}`
+ return {
+ previewUrl: res.locals.routePathname
+ ? url.resolve(`${res.locals.routePathname}/`, parcellationPreview)
+ : parcellationPreview,
+ ...p
+ }
+ }),
templateSpaces: templateSpaces.map(tmpl => {
+ const lastTemplatePath = `${encodeURIComponent(atlasId)}/template/${encodeURIComponent(tmpl['@id'])}`
return {
...tmpl,
url: res.locals.routePathname
- ? url.resolve(`${res.locals.routePathname}/${encodeURIComponent(atlasId)}/`, encodeURIComponent(tmpl['@id']))
- : `${encodeURIComponent(atlasId)}/${encodeURIComponent(tmpl['@id'])}`
+ ? url.resolve(`${res.locals.routePathname}/`, lastTemplatePath)
+ : lastTemplatePath
}
})
+
})
})
@@ -52,7 +76,7 @@ const templateIdToStringMap = new Map([
['minds/core/referencespace/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992', 'colin']
])
-router.get('/:atlasId/:templateId', async (req, res) => {
+router.get('/:atlasId/template/:templateId', async (req, res) => {
const { atlasId, templateId } = req.params
const mappedString = templateIdToStringMap.get(templateId)
@@ -69,5 +93,9 @@ router.get('/:atlasId/:templateId', async (req, res) => {
.on('error', getHandleErrorFn(req, res))
})
+router.get('/:atlasId/parcellation/:parcellationId', async (req, res) => {
+ res.status(501).end()
+})
+
module.exports = router
\ No newline at end of file
diff --git a/deploy/atlas/index.spec.js b/deploy/atlas/index.spec.js
index f30ca7bce5c65542a65d1d7b5db0b64202222931..9762c9a2076477435fdefe22488cdce0eb06e984 100644
--- a/deploy/atlas/index.spec.js
+++ b/deploy/atlas/index.spec.js
@@ -40,7 +40,7 @@ describe('atlas/index.js', () => {
const { body } = await got(`${baseUrl}/`, { responseType: 'json' })
expect(body.length).to.equal(3)
assert(
- body.every(({ url }) => !/undefined/.test(url)),
+ body.every(({ url }) => !/undefined/.test(url) ),
'url pathname should not contain undefined'
)
atlases = body
diff --git a/deploy/atlas/query.js b/deploy/atlas/query.js
index 6ecddcff312c2aa1ba30290d4c6dc11b40db0520..2523c1e814ceb1ff8e241646afc94bcdb890c2aa 100644
--- a/deploy/atlas/query.js
+++ b/deploy/atlas/query.js
@@ -22,9 +22,14 @@ const getData = async () => {
for (const file of files) {
- const data = await readFileAsync(path.join(filepath, 'atlas', file), 'utf-8')
- const json = JSON.parse(data)
- map.set(json['@id'], json)
+ try {
+
+ const data = await readFileAsync(path.join(filepath, 'atlas', file), 'utf-8')
+ const json = JSON.parse(data)
+ map.set(json['@id'], json)
+ } catch (e) {
+
+ }
}
ready = true
}
diff --git a/src/res/ext/atlas/atlas_allenMouse.json b/src/res/ext/atlas/atlas_allenMouse.json
index a882d0924e17ae07a389959b009e01d02dfd6071..f277d9f3bcf6be307511e11ee5f0b1e0b17326db 100644
--- a/src/res/ext/atlas/atlas_allenMouse.json
+++ b/src/res/ext/atlas/atlas_allenMouse.json
@@ -3,6 +3,28 @@
"name": "Allen Mouse Common Coordinate Framework v3",
"templateSpaces": [{
"@id": "minds/core/referencespace/v1.0.0/265d32a0-3d84-40a5-926f-bf89f68212b9",
- "name": "Allen Mouse Common Coordinate Framework v3"
+ "name": "Allen Mouse Common Coordinate Framework v3",
+ "availableIn": [{
+ "name": "Allen Mouse Common Coordinate Framework v3 2017",
+ "@id": "minds/core/parcellationatlas/v1.0.0/05655b58-3b6f-49db-b285-64b5a0276f83"
+ },{
+ "name": "Allen Mouse Common Coordinate Framework v3 2015",
+ "@id": "minds/core/parcellationatlas/v1.0.0/39a1384b-8413-4d27-af8d-22432225401f"
+ }]
+ }],
+ "parcellations":[{
+ "name": "Allen Mouse Common Coordinate Framework v3 2017",
+ "@id": "minds/core/parcellationatlas/v1.0.0/05655b58-3b6f-49db-b285-64b5a0276f83",
+ "availableIn": [{
+ "@id": "minds/core/referencespace/v1.0.0/265d32a0-3d84-40a5-926f-bf89f68212b9",
+ "name": "Allen Mouse Common Coordinate Framework v3"
+ }]
+ },{
+ "name": "Allen Mouse Common Coordinate Framework v3 2015",
+ "@id": "minds/core/parcellationatlas/v1.0.0/39a1384b-8413-4d27-af8d-22432225401f",
+ "availableIn": [{
+ "@id": "minds/core/referencespace/v1.0.0/265d32a0-3d84-40a5-926f-bf89f68212b9",
+ "name": "Allen Mouse Common Coordinate Framework v3"
+ }]
}]
}
\ No newline at end of file
diff --git a/src/res/ext/atlas/atlas_multiLevelHuman.json b/src/res/ext/atlas/atlas_multiLevelHuman.json
index 1fcaeb8c26fcaadd90f0495f270755ee78b8f59f..332cc2e63a0eb12d15c4ff8abebad912215bab77 100644
--- a/src/res/ext/atlas/atlas_multiLevelHuman.json
+++ b/src/res/ext/atlas/atlas_multiLevelHuman.json
@@ -1,14 +1,182 @@
{
"@id": "juelich/iav/atlas/v1.0.0/1",
"name": "Multilevel Human Atlas",
- "templateSpaces": [{
- "@id": "minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588",
- "name": "Big Brain (Histology)"
- }, {
- "@id": "minds/core/referencespace/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992",
- "name": "MNI Colin 27"
- }, {
- "@id": "minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2",
- "name": "MNI 152 ICBM 2009c Nonlinear Asymmetric"
- }]
-}
\ No newline at end of file
+ "templateSpaces": [
+ {
+ "@id": "minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588",
+ "name": "Big Brain (Histology)",
+ "avilableIn": [
+ {
+ "@id": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
+ "name": "Jülich Cytoarchitechtonic Brain Atlas (human)"
+ },
+ {
+ "name": "BigBrain Cortical Layers Segmentation",
+ "@id": "juelich/iav/atlas/v1.0.0/3"
+ },
+ {
+ "name": "Grey/White matter",
+ "@id": "juelich/iav/atlas/v1.0.0/4"
+ }
+ ]
+ },
+ {
+ "@id": "minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2",
+ "name": "MNI 152 ICBM 2009c Nonlinear Asymmetric",
+ "avilableIn": [
+ {
+ "@id": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
+ "name": "Jülich Cytoarchitechtonic Brain Atlas (human)"
+ },
+ {
+ "name": "Fibre Bundle Atlas - Long Bundle",
+ "@id": "juelich/iav/atlas/v1.0.0/5"
+ },
+ {
+ "ngId": "fibre bundle short",
+ "@id": "juelich/iav/atlas/v1.0.0/6"
+ },
+ {
+ "name": "DiFuMo Atlas (64 dimensions)",
+ "@id": "minds/core/parcellationatlas/v1.0.0/d80fbab2-ce7f-4901-a3a2-3c8ef8a3b721"
+ },
+ {
+ "name": "DiFuMo Atlas (128 dimensions)",
+ "@id": "minds/core/parcellationatlas/v1.0.0/73f41e04-b7ee-4301-a828-4b298ad05ab8"
+ },
+ {
+ "name": "DiFuMo Atlas (256 dimensions)",
+ "@id": "minds/core/parcellationatlas/v1.0.0/141d510f-0342-4f94-ace7-c97d5f160235"
+ },
+ {
+ "name": "DiFuMo Atlas (512 dimensions)",
+ "@id": "minds/core/parcellationatlas/v1.0.0/63b5794f-79a4-4464-8dc1-b32e170f3d16"
+ },
+ {
+ "name": "DiFuMo Atlas (1024 dimensions)",
+ "@id": "minds/core/parcellationatlas/v1.0.0/12fca5c5-b02c-46ce-ab9f-f12babf4c7e1"
+ }
+ ]
+ },
+ {
+ "@id": "minds/core/referencespace/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992",
+ "name": "MNI Colin 27",
+ "avilableIn": [
+ {
+ "@id": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
+ "name": "Jülich Cytoarchitechtonic Brain Atlas (human)"
+ }
+ ]
+ }
+ ],
+ "parcellations": [
+ {
+ "@id": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
+ "name": "Jülich Cytoarchitechtonic Brain Atlas (human)",
+ "avilableIn": [
+ {
+ "@id": "minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588",
+ "name": "Big Brain (Histology)"
+ },
+ {
+ "@id": "minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2",
+ "name": "MNI 152 ICBM 2009c Nonlinear Asymmetric"
+ },
+ {
+ "@id": "minds/core/referencespace/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992",
+ "name": "MNI Colin 27"
+ }
+ ]
+ },
+ {
+ "name": "BigBrain Cortical Layers Segmentation",
+ "@id": "juelich/iav/atlas/v1.0.0/3",
+ "avilableIn": [
+ {
+ "@id": "minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588",
+ "name": "Big Brain (Histology)"
+ }
+ ]
+ },
+ {
+ "name": "Grey/White matter",
+ "@id": "juelich/iav/atlas/v1.0.0/4",
+ "avilableIn": [
+ {
+ "@id": "minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588",
+ "name": "Big Brain (Histology)"
+ }
+ ]
+ },
+ {
+ "name": "Fibre Bundle Atlas - Long Bundle",
+ "@id": "juelich/iav/atlas/v1.0.0/5",
+ "avilableIn": [
+ {
+ "@id": "minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2",
+ "name": "MNI 152 ICBM 2009c Nonlinear Asymmetric"
+ }
+ ]
+ },
+ {
+ "ngId": "fibre bundle short",
+ "@id": "juelich/iav/atlas/v1.0.0/6",
+ "avilableIn": [
+ {
+ "@id": "minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2",
+ "name": "MNI 152 ICBM 2009c Nonlinear Asymmetric"
+ }
+ ]
+ },
+ {
+ "name": "DiFuMo Atlas (64 dimensions)",
+ "@id": "minds/core/parcellationatlas/v1.0.0/d80fbab2-ce7f-4901-a3a2-3c8ef8a3b721",
+ "avilableIn": [
+ {
+ "@id": "minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2",
+ "name": "MNI 152 ICBM 2009c Nonlinear Asymmetric"
+ }
+ ]
+ },
+ {
+ "name": "DiFuMo Atlas (128 dimensions)",
+ "@id": "minds/core/parcellationatlas/v1.0.0/73f41e04-b7ee-4301-a828-4b298ad05ab8",
+ "avilableIn": [
+ {
+ "@id": "minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2",
+ "name": "MNI 152 ICBM 2009c Nonlinear Asymmetric"
+ }
+ ]
+ },
+ {
+ "name": "DiFuMo Atlas (256 dimensions)",
+ "@id": "minds/core/parcellationatlas/v1.0.0/141d510f-0342-4f94-ace7-c97d5f160235",
+ "avilableIn": [
+ {
+ "@id": "minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2",
+ "name": "MNI 152 ICBM 2009c Nonlinear Asymmetric"
+ }
+ ]
+ },
+ {
+ "name": "DiFuMo Atlas (512 dimensions)",
+ "@id": "minds/core/parcellationatlas/v1.0.0/63b5794f-79a4-4464-8dc1-b32e170f3d16",
+ "avilableIn": [
+ {
+ "@id": "minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2",
+ "name": "MNI 152 ICBM 2009c Nonlinear Asymmetric"
+ }
+ ]
+ },
+ {
+ "name": "DiFuMo Atlas (1024 dimensions)",
+ "@id": "minds/core/parcellationatlas/v1.0.0/12fca5c5-b02c-46ce-ab9f-f12babf4c7e1",
+ "avilableIn": [
+ {
+ "@id": "minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2",
+ "name": "MNI 152 ICBM 2009c Nonlinear Asymmetric"
+ }
+ ]
+ }
+ ]
+}
diff --git a/src/res/ext/atlas/atlas_waxholmRat.json b/src/res/ext/atlas/atlas_waxholmRat.json
index f43a85377bd0f0caef8eb5ccf59a00552920226b..f4b9ecfef48ae3cbff429fb316f6cb767b421f0b 100644
--- a/src/res/ext/atlas/atlas_waxholmRat.json
+++ b/src/res/ext/atlas/atlas_waxholmRat.json
@@ -3,6 +3,38 @@
"name": "Waxholm Space atlas of the Sprague Dawley rat brain",
"templateSpaces": [{
"@id": "minds/core/referencespace/v1.0.0/d5717c4a-0fa1-46e6-918c-b8003069ade8",
- "name": "Waxholm Space rat brain MRI/DTI"
+ "name": "Waxholm Space rat brain MRI/DTI",
+ "availableIn": [{
+ "name": "Waxholm Space rat brain atlas v3",
+ "@id": "minds/core/parcellationatlas/v1.0.0/ebb923ba-b4d5-4b82-8088-fa9215c2e1fe"
+ },{
+ "name": "Waxholm Space rat brain atlas v2",
+ "@id": "minds/core/parcellationatlas/v1.0.0/2449a7f0-6dd0-4b5a-8f1e-aec0db03679d"
+ },{
+ "name": "Waxholm Space rat brain atlas v1",
+ "@id": "minds/core/parcellationatlas/v1.0.0/11017b35-7056-4593-baad-3934d211daba"
+ }]
+ }],
+ "parcellations": [{
+ "name": "Waxholm Space rat brain atlas v3",
+ "@id": "minds/core/parcellationatlas/v1.0.0/ebb923ba-b4d5-4b82-8088-fa9215c2e1fe",
+ "availableIn": [{
+ "@id": "minds/core/referencespace/v1.0.0/d5717c4a-0fa1-46e6-918c-b8003069ade8",
+ "name": "Waxholm Space rat brain MRI/DTI"
+ }]
+ },{
+ "name": "Waxholm Space rat brain atlas v2",
+ "@id": "minds/core/parcellationatlas/v1.0.0/2449a7f0-6dd0-4b5a-8f1e-aec0db03679d",
+ "availableIn": [{
+ "@id": "minds/core/referencespace/v1.0.0/d5717c4a-0fa1-46e6-918c-b8003069ade8",
+ "name": "Waxholm Space rat brain MRI/DTI"
+ }]
+ },{
+ "name": "Waxholm Space rat brain atlas v1",
+ "@id": "minds/core/parcellationatlas/v1.0.0/11017b35-7056-4593-baad-3934d211daba",
+ "availableIn": [{
+ "@id": "minds/core/referencespace/v1.0.0/d5717c4a-0fa1-46e6-918c-b8003069ade8",
+ "name": "Waxholm Space rat brain MRI/DTI"
+ }]
}]
-}
\ No newline at end of file
+}