diff --git a/docs/advanced/datasets.md b/docs/advanced/datasets.md
deleted file mode 100644
index 5850b315165a29e21ecb7c237fe1c5e5999f3914..0000000000000000000000000000000000000000
--- a/docs/advanced/datasets.md
+++ /dev/null
@@ -1,10 +0,0 @@
-# Fetching datasets from Knowledge Graph
-
-Human Brain Project Knowledge Graph is a metadata database consisting of datasets contributed by collaborators of the Human Brain Project and curated by human curoators in order to ensure the highest standards.
-
-!!! note
- v2.3.0 changed the way datasets are fetched from the knowledge graph.
-
-Datasets are now fetched from the knowledge graph on a region of interest basis. The fetched datasets are then filtered only on the reference space basis.
-
-Currently, only parcellation regions are supported.
diff --git a/docs/advanced/keyboard.md b/docs/advanced/keyboard.md
index d331cb87b092483f4d9fb98e1d8ffa4bd1ebfe4b..734072c77cf20cf08ca995301e255d824c424f07 100644
--- a/docs/advanced/keyboard.md
+++ b/docs/advanced/keyboard.md
@@ -1,10 +1,18 @@
# Keyboard shortcuts
-Please note that the keyboard shortcuts may alter the behaviour irreversibly.
+| Action | Desktop | Touch devices |
+| --- | --- | --- |
+| Translate / Pan | `[drag]` any of the slice views | `[drag]` any of the slice views |
+| Oblique rotation | `<shift>` + `[drag]` any of the slice views | `[rotate]` any of the slice views |
+| Zoom | `[mousewheel]` | `[pinch zoom]` |
+| Zoom | `[hover]` on any slice views > `[click]` magnifier | `[tap]` on magnifier |
+| Next slice | `<ctrl>` + `[mousewheel]` / `[p]`revious / `[n]`ext | - |
+| Next 10 slice | `<shift>` + `[mousewheel]` | - |
+| Toggle delineation | `[q]` | - |
+| Toggle cross hair | `[a]` | - |
+| Multiple region select | `<ctrl>` + `[click]` on region | - |
+| Context menu | `[right click]` | - |
-|Key|Description|
-|---|---|
-|[0-9]|Toggle layer visibility|
-|[h] [?]|Show help|
-|[o]|Toggle orthographic/perspective _3d view_ |
-|[a]|Toggle axis visibility |
+---
+
+You can enable touch interface by `[Portrait]` > `Settings` > `Enable Mobile UI`
diff --git a/docs/advanced/otherVolumes.md b/docs/advanced/otherVolumes.md
deleted file mode 100644
index b38f05425259ccdfd47e1f2e43086ec9055aa8a4..0000000000000000000000000000000000000000
--- a/docs/advanced/otherVolumes.md
+++ /dev/null
@@ -1,127 +0,0 @@
-# Displaying non-atlas volumes
-
-!!! warning
- This section is still been developed, and the content/API may change in future versions.
-
-Interactive atlas can allow for arbitary volumes to be viewed, either in the context of a reference template or without.
-
-## Viewing standalone volumes
-
-`standaloneVolumes` query param is parsed, and parsed as JSON. They are passed directly to be rendered in nehuba.
-
-If both `standaloneVolumes` and `templateSelected` are present, the latter is ignored.
-
-### Query param
-
-standaloneVolumes
-
-### Example
-```
-/?standaloneVolumes=%5B%22nifti%3A%2F%2Fhttp%3A%2F%2Flocalhost%3A1234%2Fnii.gz%22%2C%22precomputed%3A%2F%2Fhttp%3A%2F%2Flocalhost%3A4321%2Fvolume%22%5D
-```
-
-decoding and parsing as JSON:
-
-```json
-[
- "nifti://http://localhost:1234/nii.gz",
- "precomputed://http://localhost:4321/volume"
-]
-```
-
-## Viewing registered volumes
-
-`previewingDatasetFiles` query param is parsed, and parsed as JSON. Then, relevant volume information is retrieved, and displayed with `templateSelected` and `parcellationSelected`
-
-### Query param
-
-previewingDatasetFiles
-
-### Example
-
-```
-/?templateSelected=Big+Brain+%28Histology%29&parcellationSelected=Grey%2FWhite+matter&previewingDatasetFiles=%5B%7B%22datasetId%22%3A%22minds%2Fcore%2Fdataset%2Fv1.0.0%2Fb08a7dbc-7c75-4ce7-905b-690b2b1e8957%22%2C%22filename%22%3A%22Overlay%20of%20data%20modalities%22%7D%5D
-```
-
-decoding and parsing as JSON:
-
-```json
-[
- {
- "datasetId":"minds/core/dataset/v1.0.0/b08a7dbc-7c75-4ce7-905b-690b2b1e8957",
- "filename":"Overlay of data modalities"
- }
-]
-```
-
-The metadata fetched from these ID [^1] is as follows.
-
-[^1]: Currently, `kg-dataset-previewer` is used to resolve the preview URL. This is very likely going to change in the future.
-
-```json
-{
- "name": "Overlay of data modalities",
- "filename": "Overlay of data modalities",
- "mimetype": "application/json",
- "data": {
- "iav-registered-volumes": {
- "volumes": [
- {
- "name": "PLI Fiber Orientation Red Channel",
- "source": "precomputed://https://zam10143.zam.kfa-juelich.de/chumni/nifti/8b970e20de0e31b1b78ec9dba13d20319111189711983cb03ddbb7cc/BI-FOM-HSV_R",
- "shader": "void main(){ float x = toNormalized(getDataValue()); if (x < 0.1) { emitTransparent(); } else { emitRGB(vec3(1.0 * x, x * 0., 0. * x )); } }",
- "transform": [[0.7400000095367432, 0, 0, 11020745], [0, 0.2653011679649353, -0.6908077001571655, 2533286.5], [0, 0.6908077001571655, 0.2653011679649353, -32682974], [0, 0, 0, 1]],
- "opacity": 1.0
- },
- {
- "name": "PLI Fiber Orientation Green Channel",
- "source": "precomputed://https://zam10143.zam.kfa-juelich.de/chumni/nifti/8b970e20de0e31b1b78ec9dba13d20319111189711983cb03ddbb7cc/BI-FOM-HSV_G",
- "shader": "void main(){ float x = toNormalized(getDataValue()); if (x < 0.1) { emitTransparent(); } else { emitRGB(vec3(0. * x, x * 1., 0. * x )); } }",
- "transform": [[0.7400000095367432, 0, 0, 11020745], [0, 0.2653011679649353, -0.6908077001571655, 2533286.5], [0, 0.6908077001571655, 0.2653011679649353, -32682974], [0, 0, 0, 1]],
- "opacity": 0.5
- },
- {
- "name": "PLI Fiber Orientation Blue Channel",
- "source": "precomputed://https://zam10143.zam.kfa-juelich.de/chumni/nifti/8b970e20de0e31b1b78ec9dba13d20319111189711983cb03ddbb7cc/BI-FOM-HSV_B",
- "shader": "void main(){ float x = toNormalized(getDataValue()); if (x < 0.1) { emitTransparent(); } else { emitRGB(vec3(0. * x, x * 0., 1.0 * x )); } }",
- "transform": [[0.7400000095367432, 0, 0, 11020745], [0, 0.2653011679649353, -0.6908077001571655, 2533286.5], [0, 0.6908077001571655, 0.2653011679649353, -32682974], [0, 0, 0, 1]],
- "opacity": 0.25
- },
- {
- "name": "Blockface Image",
- "source": "precomputed://https://zam10143.zam.kfa-juelich.de/chumni/nifti/cb905d54437734b39807e252ef8aa68bc6ac889047fbebbafd885490/BI",
- "shader": "void main(){ float x = toNormalized(getDataValue()); if (x < 0.1) { emitTransparent(); } else { emitRGB(vec3(0.8 * x, x * 1., 0.8 * x )); } }",
- "transform": [[0.7400000095367432, 0, 0, 11020745], [0, 0.2653011679649353, -0.6908077001571655, 2533286.5], [0, 0.6908077001571655, 0.2653011679649353, -32682974], [0, 0, 0, 1]],
- "opacity": 1.0
- },
- {
- "name": "PLI Transmittance",
- "source": "precomputed://https://zam10143.zam.kfa-juelich.de/chumni/nifti/cb905d54437734b39807e252ef8aa68bc6ac889047fbebbafd885490/BI-TIM",
- "shader": "void main(){ float x = toNormalized(getDataValue()); if (x > 0.9) { emitTransparent(); } else { emitRGB(vec3(x * 1., x * 0.8, x * 0.8 )); } }",
- "transform": [[0.7400000095367432, 0, 0, 11020745], [0, 0.2653011679649353, -0.6908077001571655, 2533286.5], [0, 0.6908077001571655, 0.2653011679649353, -32682974], [0, 0, 0, 1]],
- "opacity": 1.0
- },
- {
- "name": "T2w MRI",
- "source": "precomputed://https://zam10143.zam.kfa-juelich.de/chumni/nifti/cb905d54437734b39807e252ef8aa68bc6ac889047fbebbafd885490/BI-MRI",
- "shader": "void main(){ float x = toNormalized(getDataValue()); if (x < 0.1) { emitTransparent(); } else { emitRGB(vec3(0.8 * x, 0.8 * x, x * 1. )); } }",
- "transform": [[0.7400000095367432, 0, 0, 11020745], [0, 0.2653011679649353, -0.6908077001571655, 2533286.5], [0, 0.6908077001571655, 0.2653011679649353, -32682974], [0, 0, 0, 1]],
- "opacity": 1.0
- },
- {
- "name": "MRI Labels",
- "source": "precomputed://https://zam10143.zam.kfa-juelich.de/chumni/nifti/cb905d54437734b39807e252ef8aa68bc6ac889047fbebbafd885490/BI-MRS",
- "transform": [[0.7400000095367432, 0, 0, 11020745], [0, 0.2653011679649353, -0.6908077001571655, 2533286.5], [0, 0.6908077001571655, 0.2653011679649353, -32682974], [0, 0, 0, 1]],
- "opacity": 1.0
- }
- ]
- }
- },
- "referenceSpaces": [
- {
- "name": "Big Brain (Histology)",
- "fullId": "minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588"
- }
- ]
-}
-```
diff --git a/docs/advanced/url.md b/docs/advanced/url.md
deleted file mode 100644
index d5353f6d8ccf22af54cfeb5a67e38e80aed4a3ff..0000000000000000000000000000000000000000
--- a/docs/advanced/url.md
+++ /dev/null
@@ -1,225 +0,0 @@
-# URL parsing
-
-!!! note
- Since [version 2.0.0](../releases/v2.0.0.md), navigation state and region(s) selected has been significantly redesigned.
-
- While the the URL parsing engine should still be backwards compatible, users should update their bookmarks/links.
-
-The interactive atlas viewer uses query parameters to store some of the viewer state. As a result, users can share or bookmark the URL, easily collaborating with other users in an interactive environment.
-
-
-```
-https://interactive-viewer.apps.hbp.eu/?templateSelected=Big+Brain+%28Histology%29&parcellationSelected=Cytoarchitectonic+Maps&cRegionsSelected=%7B%22interpolated%22%3A%224.5.6.7.O.P%22%7D&cNavigation=0.0.0.-W000..-J0_A.2_4alZ._DTi1.2-3oKv..7LIx..jFlG~.Efml~.M7am..10c2
-```
-
-However, expert users may want to generate custom state URLs.
-
-This document explains how the URL parsing in the Interactive Atlas Viewer work.
-
-## Query Parameters
-
-| Query param |
-| --- |
-| [`templateSelected`](#templateselected) |
-| [`parcellationSelected`](#parcellationselected) |
-| [`cNavigation`](#cnavigation) |
-| [`cRegionsSelected`](#cregionsselected) |
-
-### `templateSelected`
-
-Describes the selected template. URI encoded value of the name of the selected template.
-
-If unset, loads homepage.
-
-__Example__
-
-```
-templateSelected=Big+Brain+%28Histology%29
-```
-
-
-### `parcellationSelected`
-
-Describes the parcellation selected. Depends on `templateSelected`. URI encoded value of the name of the selected parcellation.
-
-If unset, or not a subset of parcellations supported by the selected template, the first parcellation of the selected template will be loaded instead
-
-__Example__
-
-```
-parcellationSelected=Cytoarchitectonic+Maps
-```
-
-### `cNavigation`
-
-Describes the navigation state of the viewer.
-
-Uses `..` as a delimiter for key value, `.` as a delimiter for value and [hash function](#hash-function) to encode signed float to base64 string.
-
-If unset, loads the default orientation.
-
-__Example__
-
-```
-cNavigation=0.0.0.-W000..-J0_A.2_4alZ._DTi1.2-3oKv..7LIx..jFlG~.Efml~.M7am..10c2
-```
-
-```javascript
-// cNavigation=0.0.0.-W000..-J0_A.2_4alZ._DTi1.2-3oKv..7LIx..jFlG~.Efml~.M7am..10c2
-
-const cNavigation = `0.0.0.-W000..-J0_A.2_4alZ._DTi1.2-3oKv..7LIx..jFlG~.Efml~.M7am..10c2`
-
-// First, separate with key value delimiter
-const [
- orientationStr,
- perspectiveOrientationStr,
- perspectiveZoomStr,
- positionStr,
- zoomStr
-] = cNavigation.split('..')
-
-// For entries that are Array:
-
-const orientationArr = orientationStr.split('.')
-const perspectiveOrientationArr = perspectiveOrientationStr.split('.')
-const positionArr = positionStr.split('.')
-
-
-// check hash function for decodeToNumber
-// To get values back:
-const orientation = orientationArr.map(v => decodeToNumber(v, { float: true }))
-// [ 0, 0, 0, 1 ]
-
-
-const perspectiveOrientation = perspectiveOrientationArr.map(v => decodeToNumber(v, { float: true }))
-// [ 0.7971121072769165, -0.14286760985851288, 0.17759324610233307, -0.5591617226600647 ]
-
-const zoom = decodeToNumber(zoomStr, { float: false })
-// 264578
-
-const perspectiveZoom = decodeToNumber(perspectiveZoomStr, { float: false })
-// 1922235
-
-const position = positionArr.map(v => decodeToNumber(v, { float: false }))
-// [ -11860944, -3841071, 5798192 ]
-
-```
-
-
-### `cRegionsSelected`
-
-Describe the regions selected.
-
-Query value is an URI encoded JSON object. Upon decoding, keys represent the name of the segmentation layer (which is often different to _selected parcellation_). Value is a `.` delimited array of integer [hashed](#hash-function) to base64 string.
-
-If unset, or if unable to decode, does not select region.
-
-__Example__
-
-```
-cRegionsSelected=%7B%22interpolated%22%3A%224.5.6.7.O.P%22%7D
-```
-
-```javascript
-const cRegionSelected = `%7B%22interpolated%22%3A%224.5.6.7.O.P%22%7D`
-const decoded = decodeURIComponent(cRegionSelected)
-
-const parsed = JSON.parse(decoded)
-const returnObj = {}
-for (const key in parsed){
- const seg = parsed[key].split('.').map(v => decodeToNumber(v, { float: false }))
- returnObj[key] = seg
-}
-
-// { interpolated: [ 4, 5, 6, 7, 24, 25 ] }
-
-```
-
-## hash function
-
-```javascript
-
-/**
- * First attempt at encoding int (e.g. selected region, navigation location) from number (loc info density) to b64 (higher info density)
- * The constraint is that the cipher needs to be commpatible with URI encoding
- * and a URI compatible separator is required.
- *
- * While a faster solution exist in the same post, this operation is expected to be done:
- * - once per 1 sec frequency
- * - on < 1000 numbers
- *
- * So performance is not really that important (Also, need to learn bitwise operation)
- */
-
-const cipher = '0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz_-'
-export const separator = "."
-const negString = '~'
-
-const encodeInt = number => {
- if (number % 1 !== 0) { throw new Error('cannot encodeInt on a float. Ensure float flag is set') }
- if (isNaN(Number(number)) || number === null || number === Number.POSITIVE_INFINITY) { throw new Error('The input is not valid') }
-
- let residual
- let result = ''
-
- if (number < 0) {
- result += negString
- residual = Math.floor(number * -1)
- } else {
- residual = Math.floor(number)
- }
-
- while (true) {
- result = cipher.charAt(residual % 64) + result
- residual = Math.floor(residual / 64)
-
- if (residual === 0) {
- break
- }
- }
- return result
-}
-
-const defaultB64EncodingOption = {
- float: false
-}
-
-export const encodeNumber = (number, option = defaultB64EncodingOption) => {
- const { float } = option
- if (!float) return encodeInt(number)
- else {
- const floatArray = new Float32Array(1)
- floatArray[0] = number
- const intArray = new Uint32Array(floatArray.buffer)
- const castedInt = intArray[0]
- return encodeInt(castedInt)
- }
-}
-
-const decodetoInt = encodedString => {
- let _encodedString, negFlag = false
- if (encodedString.slice(-1) === negString) {
- negFlag = true
- _encodedString = encodedString.slice(0, -1)
- } else {
- _encodedString = encodedString
- }
- return (negFlag ? -1 : 1) * [..._encodedString].reduce((acc,curr) => {
- const index = cipher.indexOf(curr)
- if (index < 0) throw new Error(`Poisoned b64 encoding ${encodedString}`)
- return acc * 64 + index
- }, 0)
-}
-
-export const decodeToNumber = (encodedString, {float = false} = defaultB64EncodingOption) => {
- if (!float) return decodetoInt(encodedString)
- else {
- const _int = decodetoInt(encodedString)
- const intArray = new Uint32Array(1)
- intArray[0] = _int
- const castedFloat = new Float32Array(intArray.buffer)
- return castedFloat[0]
- }
-}
-
-```
diff --git a/mkdocs.yml b/mkdocs.yml
index 683054e07f3097a9c1b3cc699afc0485aff729fb..22a04cd407599d49da3fc3401cec38cf4450fc80 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -29,9 +29,6 @@ nav:
- Sharing: 'usage/sharing.md'
- Advanced usage:
- Keyboard shortcuts: 'advanced/keyboard.md'
- - URL parsing: 'advanced/url.md'
- - Fetching datasets: 'advanced/datasets.md'
- - Display non-atlas volumes: 'advanced/otherVolumes.md'
- Release notes:
- v2.14.0: 'releases/v2.14.0.md'
- v2.13.5: 'releases/v2.13.5.md'
diff --git a/package-lock.json b/package-lock.json
index 988893d143b1661bf6bca7685e244e46e87c2898..b91a2cc43f2dedefcb87b50ad762cd74162b5b57 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,12 +1,12 @@
{
"name": "siibra-explorer",
- "version": "2.12.1",
+ "version": "2.14.0",
"lockfileVersion": 3,
"requires": true,
"packages": {
"": {
"name": "siibra-explorer",
- "version": "2.12.0",
+ "version": "2.14.0",
"license": "apache-2.0",
"dependencies": {
"@angular/animations": "^14.2.12",
@@ -23,7 +23,7 @@
"@ngrx/effects": "^14.3.2",
"@ngrx/store": "^14.3.2",
"acorn": "^8.4.1",
- "export-nehuba": "^0.1.0",
+ "export-nehuba": "^0.1.2",
"file-loader": "^6.2.0",
"jszip": "^3.6.0",
"postcss": "^8.3.6",
@@ -26966,9 +26966,9 @@
"dev": true
},
"node_modules/export-nehuba": {
- "version": "0.1.0",
- "resolved": "https://registry.npmjs.org/export-nehuba/-/export-nehuba-0.1.0.tgz",
- "integrity": "sha512-49mp9MiR6n+1zzeoVOfYTmr1g9CWBXrCtXK6PxwnRj+VBFrmjbp5PzBjVsGr5HsODrhwBWCLInK7zXmXaDnE/Q==",
+ "version": "0.1.2",
+ "resolved": "https://registry.npmjs.org/export-nehuba/-/export-nehuba-0.1.2.tgz",
+ "integrity": "sha512-rzydWAaa9QUKZqbYQcAuwnGsMGBlEQFD5URkEi5IGTG8LS4eH/xqc97ol0ZpUExa6jyn6nLtAjFJQmKL1rdV0w==",
"dependencies": {
"pako": "^1.0.6"
}
diff --git a/package.json b/package.json
index 101d49c59e5b92380e94010ac86ee15d81cea2fe..2aa0ea7ab4af53dcf0a1bfb695cc6c31f38f0748 100644
--- a/package.json
+++ b/package.json
@@ -66,7 +66,7 @@
"@ngrx/effects": "^14.3.2",
"@ngrx/store": "^14.3.2",
"acorn": "^8.4.1",
- "export-nehuba": "^0.1.0",
+ "export-nehuba": "^0.1.2",
"file-loader": "^6.2.0",
"jszip": "^3.6.0",
"postcss": "^8.3.6",
diff --git a/src/viewerModule/nehuba/userLayers/service.ts b/src/viewerModule/nehuba/userLayers/service.ts
index 5f9c1e130ce2ea589b26293292ccefe2be0ae915..5937a106ed53e1fa3682f2900446bba171ffcdb5 100644
--- a/src/viewerModule/nehuba/userLayers/service.ts
+++ b/src/viewerModule/nehuba/userLayers/service.ts
@@ -1,8 +1,8 @@
import { Injectable, OnDestroy } from "@angular/core"
import { MatDialog } from "@angular/material/dialog"
import { select, Store } from "@ngrx/store"
-import { concat, forkJoin, from, of, Subscription } from "rxjs"
-import { map, pairwise, switchMap } from "rxjs/operators"
+import { forkJoin, from, Subscription } from "rxjs"
+import { distinctUntilChanged, filter } from "rxjs/operators"
import {
linearTransform,
TVALID_LINEAR_XFORM_DST,
@@ -19,130 +19,241 @@ import { translateV3Entities } from "src/atlasComponents/sapi/translateV3"
import { MetaV1Schema } from "src/atlasComponents/sapi/typeV3"
type OmitKeys = "clType" | "id" | "source"
+type LayerOption = Omit<atlasAppearance.const.NgLayerCustomLayer, OmitKeys>
type Meta = {
- min?: number
- max?: number
message?: string
filename: string
}
const OVERLAY_LAYER_KEY = "x-overlay-layer"
+const OVERLAY_LAYER_PROTOCOL = `${OVERLAY_LAYER_KEY}://`
+const SUPPORTED_PREFIX = ["nifti://", "precomputed://", "swc://", "deepzoom://"] as const
+
+type ValidProtocol = typeof SUPPORTED_PREFIX[number]
+type ValidInputTypes = File|string
+
+type ProcessorOutput = {option: LayerOption, url: string, protocol: ValidProtocol, meta: Meta, cleanup: () => void}
+type ProcessResource = {
+ matcher: (input: ValidInputTypes) => boolean
+ processor: (input: ValidInputTypes) => Promise<ProcessorOutput>
+}
+
+const SOURCE_PROCESSOR: ProcessResource[] = []
+function RegisterSource(matcher: ProcessResource['matcher']) {
+ return (target: Record<string, any>, propertyKey: string, _descriptor: PropertyDescriptor) => {
+ SOURCE_PROCESSOR.push({
+ matcher,
+ processor: target[propertyKey],
+ })
+ }
+}
+
@Injectable()
export class UserLayerService implements OnDestroy {
- private userLayerUrlToIdMap = new Map<string, string>()
- private createdUrlRes = new Set<string>()
-
- private supportedPrefix = ["nifti://", "precomputed://", "swc://"]
+ #idToCleanup = new Map<string, () => void>()
- private verifyUrl(url: string) {
- for (const prefix of this.supportedPrefix) {
- if (url.includes(prefix)) return
+ static VerifyUrl(source: string) {
+ for (const prefix of SUPPORTED_PREFIX) {
+ if (source.includes(prefix)) return
}
throw new Error(
- `url: ${url} does not start with supported prefixes ${this.supportedPrefix}`
+ `source: ${source} does not start with supported prefixes ${SUPPORTED_PREFIX}`
)
}
- async getCvtFileToUrl(file: File): Promise<{
- url: string
- meta: Meta
- options?: Omit<atlasAppearance.const.NgLayerCustomLayer, OmitKeys>
- }> {
- /**
- * if extension is .swc, process as if swc
- */
- if (/\.swc$/i.test(file.name)) {
- let message = `The swc rendering is experimental. Please contact us on any feedbacks. `
- const swcText = await file.text()
- let src: TVALID_LINEAR_XFORM_SRC
- const dst: TVALID_LINEAR_XFORM_DST = "NEHUBA"
- if (/ccf/i.test(swcText)) {
- src = "CCF"
- message += `CCF detected, applying known transformation.`
- }
- if (!src) {
- message += `no known space detected. Applying default transformation.`
- }
+ @RegisterSource(
+ input => input instanceof File && input.name.endsWith(".swc")
+ )
+ async processSwc(file: File): ReturnType<ProcessResource['processor']> {
+ let message = `The swc rendering is experimental. Please contact us on any feedbacks. `
+ const swcText = await file.text()
+ let src: TVALID_LINEAR_XFORM_SRC
+ const dst: TVALID_LINEAR_XFORM_DST = "NEHUBA"
+ if (/ccf/i.test(swcText)) {
+ src = "CCF"
+ message += `CCF detected, applying known transformation.`
+ }
+ if (!src) {
+ message += `no known space detected. Applying default transformation.`
+ }
- const xform = await linearTransform(src, dst)
+ const xform = await linearTransform(src, dst)
+ const url = URL.createObjectURL(file)
- const url = URL.createObjectURL(file)
- this.createdUrlRes.add(url)
+ return {
+ option: {
+ type: 'segmentation',
+ transform: xform,
+ segments: ["1"]
+ },
+ url,
+ protocol: "swc://",
+ meta: {
+ filename: file.name
+ },
+ cleanup: () => URL.revokeObjectURL(url)
+ }
+ }
- return {
- url: `swc://${url}`,
- meta: {
- filename: file.name,
- message,
- },
- options: {
- segments: ["1"],
- transform: xform,
- type: "segmentation"
- },
- }
+ async #processUnpackedNiiBuf(buf: ArrayBuffer): ReturnType<ProcessResource['processor']> {
+ const { result } = await this.worker.sendMessage({
+ method: "PROCESS_NIFTI",
+ param: {
+ nifti: buf,
+ },
+ transfers: [buf],
+ })
+ const { buffer, meta } = result
+ const url = URL.createObjectURL(new Blob([buffer]))
+ return {
+ protocol: 'nifti://',
+ url,
+ option: {
+ type: 'image',
+ shader: getShader({
+ colormap: EnumColorMapName.MAGMA,
+ lowThreshold: meta.min || 0,
+ highThreshold: meta.max || 1,
+ })
+ },
+ meta,
+ cleanup: () => URL.revokeObjectURL(url)
}
+ }
- /**
- * process as if nifti
- */
+ @RegisterSource(
+ input => input instanceof File && input.name.endsWith(".nii")
+ )
+ async processNifti(file: File){
+ const buf = await file.arrayBuffer()
+ return await this.#processUnpackedNiiBuf(buf)
+ }
- // Get file, try to inflate, if files, use original array buffer
+ @RegisterSource(
+ input => input instanceof File && input.name.endsWith(".nii.gz")
+ )
+ async processNiiGz(file: File) {
const buf = await file.arrayBuffer()
- let outbuf
try {
const { pako } = await getExportNehuba()
- outbuf = pako.inflate(buf).buffer
+ const outbuf = pako.inflate(buf).buffer
+ return await this.#processUnpackedNiiBuf(outbuf)
} catch (e) {
console.log("unpack error", e)
- outbuf = buf
+ throw e
}
+ }
- const { result } = await this.worker.sendMessage({
- method: "PROCESS_NIFTI",
- param: {
- nifti: outbuf,
- },
- transfers: [outbuf],
- })
+ @RegisterSource(
+ input => typeof input === "string" && input.startsWith(OVERLAY_LAYER_PROTOCOL)
+ )
+ async processOverlayPath(source: string) {
+ const strippedSrc = source.replace(OVERLAY_LAYER_PROTOCOL, "")
+ const { cleanup, ...rest } = await this.#processInput(strippedSrc)
+ return {
+ ...rest,
+ cleanup: () => {
+ this.routerSvc.setCustomRoute(OVERLAY_LAYER_KEY, null)
+ cleanup()
+ }
+ }
+ }
- const { meta, buffer } = result
+ @RegisterSource(
+ input => typeof input === "string" && input.startsWith("precomputed://")
+ )
+ async processPrecomputed(source: string): Promise<ProcessorOutput>{
+ const url = source.replace("precomputed://", "")
+ const { transform, meta } = await forkJoin({
+ transform: fetch(`${url}/transform.json`)
+ .then(res => res.json() as Promise<MetaV1Schema["transform"]>)
+ .catch(_e => null as MetaV1Schema["transform"]),
+ meta: from(
+ translateV3Entities.fetchMeta(url)
+ .catch(_e => null as MetaV1Schema)
+ )
+ }).toPromise()
+
+ return {
+ cleanup: () => {},
+ meta: {
+ filename: url
+ },
+ option: {
+ transform: meta?.transform || transform,
+ shader: getShaderFromMeta(meta),
+ },
+ protocol: "precomputed://",
+ url
+ }
+ }
- const url = URL.createObjectURL(new Blob([buffer]))
+ @RegisterSource(
+ input => typeof input === "string" && input.startsWith("deepzoom://")
+ )
+ async processDzi(source: string): Promise<ProcessorOutput> {
+ const url = source.replace("deepzoom://", "")
+ const scaleFactor = 1e2
return {
- url: `nifti://${url}`,
+ cleanup: () => {},
meta: {
- filename: file.name,
- min: meta.min || 0,
- max: meta.max || 1,
- message: meta.message,
+ filename: `deepzoom://${url}`
},
- options: {
- shader: getShader({
- colormap: EnumColorMapName.MAGMA,
- lowThreshold: meta.min || 0,
- highThreshold: meta.max || 1,
- }),
- type: 'image'
+ option: {
+ transform: [
+ [ scaleFactor, 0, 0, 0 ],
+ [ 0, scaleFactor, 0, 0 ],
+ [ 0, 0, 1, 0 ],
+ [ 0, 0, 0, 1 ],
+ ],
+ shader: `void main(){emitRGB(vec3(toNormalized(getDataValue(0)),toNormalized(getDataValue(1)),toNormalized(getDataValue(2))));}`,
},
+ protocol: "deepzoom://",
+ url
}
}
+ async #processInput(input: ValidInputTypes): Promise<ProcessorOutput> {
+ for (const { matcher, processor } of SOURCE_PROCESSOR) {
+ if (matcher(input)) {
+ return await processor.apply(this, [input])
+ }
+ }
+ debugger
+ const inputStr = input instanceof File
+ ? input.name
+ : input
+ throw new Error(`Could not find a processor for ${inputStr}`)
+ }
+
+ async handleUserInput(input: ValidInputTypes){
+ const id = getUuid()
+ const { option, protocol, url, meta, cleanup } = await this.#processInput(input)
+ if (this.#idToCleanup.has(id)) {
+ throw new Error(`${url} was already registered`)
+ }
+ this.#idToCleanup.set(id, cleanup)
+ this.addUserLayer(
+ id,
+ `${protocol}${url}`,
+ meta,
+ option,
+ )
+ return
+ }
+
addUserLayer(
- url: string,
+ id: string,
+ source: string,
meta: Meta,
- options: Omit<atlasAppearance.const.NgLayerCustomLayer, OmitKeys> = {}
+ options: LayerOption = {}
) {
- this.verifyUrl(url)
- if (this.userLayerUrlToIdMap.has(url)) {
- throw new Error(`url ${url} already added`)
- }
- const id = getUuid()
- const layer: atlasAppearance.const.NgLayerCustomLayer = {
+ UserLayerService.VerifyUrl(source)
+ const layer = {
id,
- clType: "customlayer/nglayer",
- source: url,
+ clType: "customlayer/nglayer" as const,
+ source,
...options,
}
this.store$.dispatch(
@@ -151,48 +262,30 @@ export class UserLayerService implements OnDestroy {
})
)
- this.userLayerUrlToIdMap.set(url, id)
-
- this.dialog
- .open(UserLayerInfoCmp, {
- data: {
- layerName: id,
- filename: meta.filename,
- min: meta.min || 0,
- max: meta.max || 1,
- warning: [meta.message] || [],
- },
- hasBackdrop: false,
- disableClose: true,
- position: {
- top: "0em",
- },
- autoFocus: false,
- panelClass: ["no-padding-dialog", "w-100"],
- })
- .afterClosed()
- .subscribe(() => {
- this.routerSvc.setCustomRoute(OVERLAY_LAYER_KEY, null)
- })
- }
-
- removeUserLayer(url: string) {
- if (!this.userLayerUrlToIdMap.has(url)) {
- throw new Error(`${url} has not yet been added.`)
- }
-
- /**
- * if the url to be removed is a url resource, revoke the resource
- */
- const matched = /http.*$/.exec(url)
- if (matched && this.createdUrlRes.has(matched[0])) {
- URL.revokeObjectURL(matched[0])
- this.createdUrlRes.delete(matched[0])
- }
-
- const id = this.userLayerUrlToIdMap.get(url)
- this.store$.dispatch(atlasAppearance.actions.removeCustomLayer({ id }))
- this.userLayerUrlToIdMap.delete(url)
+ this.dialog.open(UserLayerInfoCmp, {
+ data: {
+ layerName: id,
+ filename: meta.filename,
+ warning: [meta.message] || [],
+ },
+ hasBackdrop: false,
+ disableClose: true,
+ position: {
+ top: "0em",
+ },
+ autoFocus: false,
+ panelClass: ["no-padding-dialog", "w-100"],
+ })
+ .afterClosed()
+ .subscribe(() => {
+ this.store$.dispatch(atlasAppearance.actions.removeCustomLayer({ id }))
+ const cleanup = this.#idToCleanup.get(id)
+ if (!cleanup) {
+ console.warn(`idToCleanup ${id} could not be found! ${meta.filename}`)
+ return
+ }
+ cleanup()
+ })
}
#subscription: Subscription[] = []
@@ -203,66 +296,12 @@ export class UserLayerService implements OnDestroy {
private routerSvc: RouterService
) {
this.#subscription.push(
- concat(
- of(null as string),
- this.routerSvc.customRoute$.pipe(
- select(v => v[OVERLAY_LAYER_KEY])
- )
+ this.routerSvc.customRoute$.pipe(
+ select(v => v[OVERLAY_LAYER_KEY])
).pipe(
- pairwise(),
- switchMap(([prev, curr]) => {
- /**
- * for precomputed sources, check if transform.json exists.
- * if so, try to fetch it, and set it as transform
- */
- if (!curr) {
- return of({ prev, curr, meta: null as MetaV1Schema })
- }
- if (!curr.startsWith("precomputed://")) {
- return of({ prev, curr, meta: null as MetaV1Schema })
- }
- const url = curr.replace("precomputed://", "")
-
-
- return forkJoin({
- transform: fetch(`${url}/transform.json`)
- .then(res => res.json() as Promise<MetaV1Schema["transform"]>)
- .catch(_e => null as MetaV1Schema["transform"]),
- meta: from(
- translateV3Entities.fetchMeta(url)
- .catch(_e => null as MetaV1Schema)
- )
- }).pipe(
- map(({ transform, meta }) => {
- return {
- prev,
- curr,
- meta: {
- ...meta,
- transform: meta?.transform || transform
- }
- }
- }),
- )
- })
- ).subscribe(({ prev, curr, meta }) => {
- if (prev) {
- this.removeUserLayer(prev)
- }
- if (curr) {
- this.addUserLayer(
- curr,
- {
- filename: curr,
- message: `Overlay layer populated in URL`,
- },
- {
- shader: getShaderFromMeta(meta),
- transform: meta.transform
- }
- )
- }
- })
+ distinctUntilChanged(),
+ filter(url => !!url)
+ ).subscribe(url => this.handleUserInput(url))
)
}
diff --git a/src/viewerModule/nehuba/userLayers/userlayerDragdrop.directive.spec.ts b/src/viewerModule/nehuba/userLayers/userlayerDragdrop.directive.spec.ts
index be2c332759205abf28aa9d844244a325a7a5a106..d3724c1e2a6134973661e30578df71d3a9deafa2 100644
--- a/src/viewerModule/nehuba/userLayers/userlayerDragdrop.directive.spec.ts
+++ b/src/viewerModule/nehuba/userLayers/userlayerDragdrop.directive.spec.ts
@@ -17,10 +17,7 @@ class TestCmp {
describe("dragdrop.directive.spec.ts", () => {
let fixture: ComponentFixture<TestCmp>
-
- let addUserLayerSpy: jasmine.Spy
- let removeUserLayerSpy: jasmine.Spy
- let getCvtFileToUrlSpy: jasmine.Spy
+ let handleUserInputSpy: jasmine.Spy
let dummyFile1: File
let dummyFile2: File
@@ -42,18 +39,14 @@ describe("dragdrop.directive.spec.ts", () => {
useValue: {
addUserLayer: () => {},
removeUserLayer: () => {},
- getCvtFileToUrl: () => Promise.resolve(),
+ handleUserInput: () => Promise.resolve(),
},
},
],
})
const svc = TestBed.inject(UserLayerService)
-
- addUserLayerSpy = spyOn(svc, "addUserLayer")
- removeUserLayerSpy = spyOn(svc, "removeUserLayer")
- getCvtFileToUrlSpy = spyOn(svc, "getCvtFileToUrl")
-
- getCvtFileToUrlSpy.and.resolveTo({ meta, url, options })
+ handleUserInputSpy = spyOn(svc, "handleUserInput")
+ handleUserInputSpy.and.resolveTo(null)
fixture = TestBed.createComponent(TestCmp)
fixture.detectChanges()
@@ -73,9 +66,7 @@ describe("dragdrop.directive.spec.ts", () => {
})()
})
afterEach(() => {
- addUserLayerSpy.calls.reset()
- removeUserLayerSpy.calls.reset()
- getCvtFileToUrlSpy.calls.reset()
+ handleUserInputSpy.calls.reset()
})
describe("> malformed input", () => {
@@ -99,7 +90,7 @@ describe("dragdrop.directive.spec.ts", () => {
})
it("> should not call addnglayer", () => {
- expect(getCvtFileToUrlSpy).not.toHaveBeenCalled()
+ expect(handleUserInputSpy).not.toHaveBeenCalled()
})
// TODO having a difficult time getting snackbar harness
@@ -128,17 +119,11 @@ describe("dragdrop.directive.spec.ts", () => {
})
it("> should call addNgLayer", () => {
- expect(getCvtFileToUrlSpy).toHaveBeenCalledTimes(1)
- const arg = getCvtFileToUrlSpy.calls.argsFor(0)
+ expect(handleUserInputSpy).toHaveBeenCalledTimes(1)
+ const arg = handleUserInputSpy.calls.argsFor(0)
expect(arg.length).toEqual(1)
expect(arg[0]).toEqual(dummyFile1)
- expect(addUserLayerSpy).toHaveBeenCalledTimes(1)
- const args1 = addUserLayerSpy.calls.argsFor(0)
-
- expect(args1[0]).toBe(url)
- expect(args1[1]).toBe(meta)
- expect(args1[2]).toBe(options)
})
})
})
diff --git a/src/viewerModule/nehuba/userLayers/userlayerDragdrop.directive.ts b/src/viewerModule/nehuba/userLayers/userlayerDragdrop.directive.ts
index a56d677fd8b77ecce210dc7c2940ea7b1836472b..2b049c7f70b4f011f45d99b7f09bbb808e088d5a 100644
--- a/src/viewerModule/nehuba/userLayers/userlayerDragdrop.directive.ts
+++ b/src/viewerModule/nehuba/userLayers/userlayerDragdrop.directive.ts
@@ -53,9 +53,6 @@ export class UserLayerDragDropDirective
return
}
const file = files[0]
-
- const { meta, url, options } = await this.svc.getCvtFileToUrl(file)
-
- this.svc.addUserLayer(url, meta, options)
+ await this.svc.handleUserInput(file)
}
}
diff --git a/src/viewerModule/nehuba/userLayers/userlayerInfo/userlayerInfo.component.ts b/src/viewerModule/nehuba/userLayers/userlayerInfo/userlayerInfo.component.ts
index 204da49bf5170ca9998ed52f26fc31ad1df05471..eb4f6fac154934c88b3c83e595430046b2e2b770 100644
--- a/src/viewerModule/nehuba/userLayers/userlayerInfo/userlayerInfo.component.ts
+++ b/src/viewerModule/nehuba/userLayers/userlayerInfo/userlayerInfo.component.ts
@@ -8,8 +8,6 @@ import { MediaQueryDirective } from "src/util/directives/mediaQuery.directive";
export type UserLayerInfoData = {
layerName: string
filename: string
- min: number
- max: number
warning: string[]
}
diff --git a/src/viewerModule/nehuba/userLayers/userlayerInfo/userlayerInfo.template.html b/src/viewerModule/nehuba/userLayers/userlayerInfo/userlayerInfo.template.html
index c999b1c1befd8d650096bf38c6b23a8aadf63192..84b908d46b466d47be99763d6bd3147a1423260e 100644
--- a/src/viewerModule/nehuba/userLayers/userlayerInfo/userlayerInfo.template.html
+++ b/src/viewerModule/nehuba/userLayers/userlayerInfo/userlayerInfo.template.html
@@ -55,8 +55,6 @@
<ng-layer-tune
[hideCtrl]="onlyOpacity ? HIDE_NG_TUNE_CTRL.ONLY_SHOW_OPACITY : ''"
advanced-control="true"
- [ngLayerName]="data.layerName"
- [thresholdMin]="data.min"
- [thresholdMax]="data.max">
+ [ngLayerName]="data.layerName">
</ng-layer-tune>
</ng-template>