processed metadata

code/generate_metadata/.gitignore

@@ -0,0 +1 @@
+node_modules

code/generate_metadata/package-lock.json

@@ -0,0 +1,232 @@
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+}

code/generate_metadata/package.json

@@ -0,0 +1,16 @@
+{
+  "name": "generate_metadata",
+  "version": "1.0.0",
+  "description": "",
+  "main": "index.js",
+  "scripts": {
+    "test": "echo \"Error: no test specified\" && exit 1"
+  },
+  "keywords": [],
+  "author": "",
+  "license": "ISC",
+  "dependencies": {
+    "csv-parse": "^4.10.1",
+    "got": "^11.3.0"
+  }
+}

code/generate_metadata/script.js

@@ -0,0 +1,138 @@
+const got = require('got')
+const csv = require('csv-parse/lib/sync')
+const fs = require('fs')
+const path = require('path')
+const { execSync } = require('child_process')
+
+const kgInfoApi = `https://interactive-viewer.apps.hbp.eu/datasets/kgInfo`
+const ngRoot = `https://neuroglancer.humanbrainproject.eu/precomputed/difumo/pmaps/`
+const outputPath = path.join(__dirname, '../../output/taxonomy_metadata')
+const inputPath = path.join(__dirname, '../../input')
+
+const datasets = [
+  ['DiFuMo atlas (64 dimensions)',   'https://kg.ebrains.eu/search/instances/Dataset/e472a8c7-d9f9-4e75-9d0b-b137cecbc6a2'],
+  ['DiFuMo atlas (128 dimensions)',  'https://kg.ebrains.eu/search/instances/Dataset/b8d0ba16-5543-4594-a6f0-ecbacfc9fb04'],
+  ['DiFuMo atlas (256 dimensions)',  'https://kg.ebrains.eu/search/instances/Dataset/5438792c-ff2a-4554-9f85-af795f870741'],
+  ['DiFuMo atlas (512 dimensions)',  'https://kg.ebrains.eu/search/instances/Dataset/2ab064dd-7ac5-44ca-8711-a72435f0672e'],
+  ['DiFuMo atlas (1024 dimensions)', 'https://kg.ebrains.eu/search/instances/Dataset/164ef5c9-bec5-43c7-b258-80798cb0d57b']
+]
+
+const getKgId = fullId => {
+  const re = /\/([a-f0-9-]*)$/.exec(fullId)
+  return re && re[1]
+} 
+
+const kgIds = datasets.map(arr => {
+  const re = /\(([0-9]*)\sdimensions\)$/.exec(arr[0])
+  return {
+    key: re[1],
+    kgId: getKgId(arr[1])
+  }
+})
+
+const getKgInfo = async kgId => {
+  const resp = await got(kgInfoApi, {
+    responseType: 'json',
+    searchParams: {
+      kgSchema: 'minds/core/dataset/v1.0.0',
+      kgId
+    }
+  })
+  return resp.body
+}
+
+const main = async () => {
+  for (const {kgId, key} of kgIds) {
+    const r = await getKgInfo(kgId)
+    const labelFile = r.files.find(file => /^labels_[0-9]*_dictionary\.csv$/.test(file.name))
+    if (!labelFile) throw new Error('labelFile not found')
+
+    const { body: labelFileContent } = await got(labelFile.absolutePath, { responseType: 'text' })
+    const arr = csv(labelFileContent, {
+      comment: '#',
+      columns: true
+    })
+    
+    const regions = []
+    const files = []
+    for (const { Component, Difumo_names, ...rest } of arr) {
+
+      /**
+       * region metadata to be interpreted by the viewer
+       */
+      const region = {
+        name: Difumo_names,
+        labelIndex: Component,
+        originDatasets: [
+          {
+            kgId,
+            kgSchema: 'minds/core/dataset/v1.0.0',
+            filename: `${Component}.nii.gz`
+          }
+        ],
+        ontologyMetadata: rest
+      }
+      regions.push(region)
+
+      /**
+       * preview metadata to be interpreted by viewer and kg previewer data
+       */
+
+      const volumeMetadata = JSON.parse(fs.readFileSync(
+        path.join(outputPath, '../metadata', key, `${Number(Component) - 1}.nii.gz.json`),
+        'utf-8'
+      ))
+
+       const file = {
+         filename: `${Component}.nii.gz`,
+         mimetype: 'application/nifti',
+         url: `${ngRoot}${key}/${Component}.nii.gz`,
+         referenceSpaces: [
+          {
+            name: "MNI 152 ICBM 2009c Nonlinear Asymmetric",
+            fullId: "minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2"
+          }
+        ],
+        volumeMetadata
+       }
+       files.push(file)
+    }
+
+    /**
+     * iterated over all files, now write to json
+     */
+    fs.writeFileSync(
+      path.join(outputPath, 'datasetpreview_metadata',  kgId),
+      JSON.stringify(files, null, 2),
+      'utf-8'
+    )
+
+    const difumoParcellation = {
+      name: `DiFuMo Atlas (${key} dimensions)`,
+      ngId: `DiFuMo Atlas (${key} dimensions)`,
+      auxillaryMeshIndices: [
+        65535
+      ],
+      originDatasets: [
+        {
+          kgSchema: "minds/core/dataset/v1.0.0",
+          kgId
+        }
+      ],
+      regions
+    }
+    fs.writeFileSync(
+      path.join(outputPath, 'taxonomy_metadata', `difumo_${key}.json`),
+      JSON.stringify(difumoParcellation, null, 2),
+      'utf-8'
+    )
+  }
+}
+
+execSync(`rm -rf ${outputPath}/*`)
+
+execSync(`mkdir -p ${outputPath}/taxonomy_metadata`)
+execSync(`mkdir -p ${outputPath}/datasetpreview_metadata`)
+
+
+main()

output/taxonomy_metadata/datasetpreview_metadata/e472a8c7-d9f9-4e75-9d0b-b137cecbc6a2

@@ -0,0 +1,962 @@
+[
+  {
+    "filename": "1.nii.gz",
+    "mimetype": "application/nifti",
+    "url": "https://neuroglancer.humanbrainproject.eu/precomputed/difumo/pmaps/64/1.nii.gz",
+    "referenceSpaces": [
+      {
+        "name": "MNI 152 ICBM 2009c Nonlinear Asymmetric",
+        "fullId": "minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2"
+      }
+    ],
+    "volumeMetadata": {
+      "max": 0.0007505516987293959,
+      "min": 0
+    }
+  },
+  {
+    "filename": "2.nii.gz",
+    "mimetype": "application/nifti",
+    "url": "https://neuroglancer.humanbrainproject.eu/precomputed/difumo/pmaps/64/2.nii.gz",
+    "referenceSpaces": [
+      {
+        "name": "MNI 152 ICBM 2009c Nonlinear Asymmetric",
+        "fullId": "minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2"
+      }
+    ],
+    "volumeMetadata": {
+      "max": 0.0007111851591616869,
+      "min": 0
+    }
+  },
+  {
+    "filename": "3.nii.gz",
+    "mimetype": "application/nifti",
+    "url": "https://neuroglancer.humanbrainproject.eu/precomputed/difumo/pmaps/64/3.nii.gz",
+    "referenceSpaces": [
+      {
+        "name": "MNI 152 ICBM 2009c Nonlinear Asymmetric",
+        "fullId": "minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2"
+      }
+    ],
+    "volumeMetadata": {
+      "max": 0.0010291269281879067,
+      "min": 0
+    }
+  },
+  {
+    "filename": "4.nii.gz",
+    "mimetype": "application/nifti",
+    "url": "https://neuroglancer.humanbrainproject.eu/precomputed/difumo/pmaps/64/4.nii.gz",
+    "referenceSpaces": [
+      {
+        "name": "MNI 152 ICBM 2009c Nonlinear Asymmetric",
+        "fullId": "minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2"
+      }
+    ],
+    "volumeMetadata": {
+      "max": 0.0011246243957430124,
+      "min": 0
+    }
+  },
+  {
+    "filename": "5.nii.gz",
+    "mimetype": "application/nifti",
+    "url": "https://neuroglancer.humanbrainproject.eu/precomputed/difumo/pmaps/64/5.nii.gz",
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scripts/s.sh

@@ -1,11 +0,0 @@
-#! /bin/bash
-
-for f in $(find . -name '*.nii.gz'); do
-  strip_prefix=${f#./};
-  num_name=${strip_prefix%.nii.gz}
-  mv $f ./$((num_name + 1))_.nii.gz;
-done
-
-for f in $(find . -name '*.nii.gz'); do
-  mv $f ${f%_.nii.gz}.nii.gz;
-done