From a09bdb36e482aabdd88de6b9c4405b696e22d56b Mon Sep 17 00:00:00 2001 From: Alexander Serdyukov Date: Wed, 22 Apr 2026 05:21:24 +0400 Subject: [PATCH 1/6] Tried adding .hic conversion using hictk --- src/app/core/net/api/RequestManager.ts | 18 ++ src/app/core/net/api/request.ts | 10 + src/app/core/net/api/response.ts | 28 +++ src/app/core/net/dto/responseDTO.ts | 31 +++ .../upper_ribbon/CoolerConverter.vue | 190 +++++++++++++++++- .../components/upper_ribbon/NavigationBar.vue | 13 +- .../converter/ConverterStatusChecker.vue | 81 +++++++- .../converter/CoolerFileSelector.vue | 4 +- 8 files changed, 354 insertions(+), 21 deletions(-) diff --git a/src/app/core/net/api/RequestManager.ts b/src/app/core/net/api/RequestManager.ts index 3288288..bc63ad6 100644 --- a/src/app/core/net/api/RequestManager.ts +++ b/src/app/core/net/api/RequestManager.ts @@ -29,6 +29,7 @@ import { import { HiCTAPIRequestDTO } from "../dto/requestDTO"; import { ConversionJobResponseDTO, + ConversionToolchainStatusResponseDTO, CurrentSignalRangeResponseDTO, FastaLinkResponseDTO, NameMappingResponseDTO, @@ -52,6 +53,7 @@ import { LinkFASTARequest, ListAGPFilesRequest, ListCoolerFilesRequest, + ListConvertibleMatrixFilesRequest, ListFilesDetailedRequest, ListFASTAFilesRequest, ListFilesRequest, @@ -70,6 +72,7 @@ import { StartConversionJobRequest, ListConversionJobsRequest, GetConversionJobRequest, + GetConversionToolchainStatusRequest, StopConversionJobRequest, RenameContigRequest, RenameScaffoldRequest, @@ -103,6 +106,7 @@ import { } from "./request"; import { ConversionJobResponse, + ConversionToolchainStatusResponse, CurrentSignalRangeResponse, FastaLinkResponse, FileEntryResponse, @@ -398,6 +402,13 @@ class RequestManager { return response.data as string[]; } + public async listConvertibleMatrices(): Promise { + const response = await this.sendRequest( + new ListConvertibleMatrixFilesRequest() + ); + return response.data as string[]; + } + public async listTrackFiles(): Promise { const response = await this.sendRequest(new ListTrackFilesRequest()); return response.data as string[]; @@ -688,6 +699,13 @@ class RequestManager { ); } + public async getConversionToolchainStatus(): Promise { + return this.sendRequest(new GetConversionToolchainStatusRequest()).then( + (response) => + new ConversionToolchainStatusResponseDTO(response.data).toEntity() + ); + } + public async renameContig( contigId: number, newName: string | null diff --git a/src/app/core/net/api/request.ts b/src/app/core/net/api/request.ts index 696b7e6..b482460 100644 --- a/src/app/core/net/api/request.ts +++ b/src/app/core/net/api/request.ts @@ -73,6 +73,10 @@ class ListCoolerFilesRequest implements HiCTAPIRequest { requestPath = "/list_coolers"; } +class ListConvertibleMatrixFilesRequest implements HiCTAPIRequest { + requestPath = "/list_convertible_matrices"; +} + class ListTrackFilesRequest implements HiCTAPIRequest { requestPath = "/tracks/list_files"; } @@ -205,6 +209,10 @@ class StopConversionJobRequest implements HiCTAPIRequest { } } +class GetConversionToolchainStatusRequest implements HiCTAPIRequest { + requestPath = "/convert/toolchain"; +} + class SetContrastRangeRequest implements HiCTAPIRequest { requestPath = "/set_contrast_range"; @@ -546,11 +554,13 @@ export { AttachSessionRequest, CloseFileRequest, ListCoolerFilesRequest, + ListConvertibleMatrixFilesRequest, StartConversionJobRequest, StartBatchConversionJobsRequest, ListConversionJobsRequest, GetConversionJobRequest, StopConversionJobRequest, + GetConversionToolchainStatusRequest, RenameContigRequest, RenameScaffoldRequest, ExportNameMappingRequest, diff --git a/src/app/core/net/api/response.ts b/src/app/core/net/api/response.ts index 3ad4e51..dc5cbf1 100644 --- a/src/app/core/net/api/response.ts +++ b/src/app/core/net/api/response.ts @@ -42,6 +42,10 @@ class ConversionJobResponse { public readonly sourceFilename: string, public readonly outputFilename: string, public readonly direction: string, + public readonly currentStage: string, + public readonly currentStageLabel: string, + public readonly stageDetail: string, + public readonly stageProgress: number, public readonly overallProgress: number, public readonly resolutionProgress: number, public readonly currentResolution: number, @@ -51,11 +55,34 @@ class ConversionJobResponse { public readonly resolutionEtaMillis: number, public readonly inputSizeBytes: number, public readonly outputSizeBytes: number, + public readonly toolchainSource: string, + public readonly toolchainSummary: string, + public readonly toolchainNotices: string[], + public readonly toolchainCitations: string[], public readonly logs: string[], public readonly error: string ) {} } +class ConversionToolchainStatusResponse { + public constructor( + public readonly platform: string, + public readonly source: string, + public readonly supportedPlatform: boolean, + public readonly hicConversionAvailable: boolean, + public readonly hictkAvailable: boolean, + public readonly hictkCommand: string | null, + public readonly coolerAvailable: boolean, + public readonly coolerCommand: string | null, + public readonly pythonAvailable: boolean, + public readonly pythonCommand: string | null, + public readonly summary: string, + public readonly notices: string[], + public readonly citations: string[], + public readonly limitations: string[] + ) {} +} + class NameMappingResponse { public constructor( public readonly contigs: { @@ -301,6 +328,7 @@ export { CurrentSignalRangeResponse, TilePOSTResponse, ConversionJobResponse, + ConversionToolchainStatusResponse, NameMappingResponse, TrackSummaryResponse, TrackBinBlockResponse, diff --git a/src/app/core/net/dto/responseDTO.ts b/src/app/core/net/dto/responseDTO.ts index e2c79b3..ebb1b06 100644 --- a/src/app/core/net/dto/responseDTO.ts +++ b/src/app/core/net/dto/responseDTO.ts @@ -21,6 +21,7 @@ import { ConversionJobResponse, + ConversionToolchainStatusResponse, CurrentSignalRangeResponse, FileEntryResponse, FastaLinkCompatibilityResponse, @@ -95,6 +96,10 @@ class ConversionJobResponseDTO extends InboundDTO { this.json["sourceFilename"] as string, this.json["outputFilename"] as string, this.json["direction"] as string, + (this.json["currentStage"] as string) ?? "", + (this.json["currentStageLabel"] as string) ?? "", + (this.json["stageDetail"] as string) ?? "", + (this.json["stageProgress"] as number) ?? 0, this.json["overallProgress"] as number, this.json["resolutionProgress"] as number, this.json["currentResolution"] as number, @@ -104,12 +109,37 @@ class ConversionJobResponseDTO extends InboundDTO { this.json["resolutionEtaMillis"] as number, this.json["inputSizeBytes"] as number, this.json["outputSizeBytes"] as number, + (this.json["toolchainSource"] as string) ?? "", + (this.json["toolchainSummary"] as string) ?? "", + (this.json["toolchainNotices"] as string[]) ?? [], + (this.json["toolchainCitations"] as string[]) ?? [], (this.json["logs"] as string[]) ?? [], (this.json["error"] as string) ?? "" ); } } +class ConversionToolchainStatusResponseDTO extends InboundDTO { + public toEntity(): ConversionToolchainStatusResponse { + return new ConversionToolchainStatusResponse( + (this.json["platform"] as string) ?? "unknown", + (this.json["source"] as string) ?? "unknown", + Boolean(this.json["supportedPlatform"] ?? false), + Boolean(this.json["hicConversionAvailable"] ?? false), + Boolean(this.json["hictkAvailable"] ?? false), + (this.json["hictkCommand"] as string) ?? null, + Boolean(this.json["coolerAvailable"] ?? false), + (this.json["coolerCommand"] as string) ?? null, + Boolean(this.json["pythonAvailable"] ?? false), + (this.json["pythonCommand"] as string) ?? null, + (this.json["summary"] as string) ?? "", + (this.json["notices"] as string[]) ?? [], + (this.json["citations"] as string[]) ?? [], + (this.json["limitations"] as string[]) ?? [] + ); + } +} + class NameMappingResponseDTO extends InboundDTO { public toEntity(): NameMappingResponse { return new NameMappingResponse( @@ -421,6 +451,7 @@ export { CurrentSignalRangeResponseDTO, TilePOSTResponseDTO, ConversionJobResponseDTO, + ConversionToolchainStatusResponseDTO, NameMappingResponseDTO, TrackSummaryResponseDTO, TrackQueryResponseDTO, diff --git a/src/app/ui/components/upper_ribbon/CoolerConverter.vue b/src/app/ui/components/upper_ribbon/CoolerConverter.vue index 84291cb..2e1da1a 100644 --- a/src/app/ui/components/upper_ribbon/CoolerConverter.vue +++ b/src/app/ui/components/upper_ribbon/CoolerConverter.vue @@ -29,9 +29,9 @@ data-backdrop="static" >
-
+
-
Convert Coolers for HiCT
+
Convert matrix files for HiCT
+
+
+ External .hic conversion toolchain + + {{ + toolchainStatus.hicConversionAvailable + ? "available" + : "unavailable" + }} + + loading… +
+

{{ toolchainStatus.summary }}

+

+ {{ limitation }} +

+

+ {{ notice }} +

+
+

+ Output: {{ deriveOutputFilename(selectedCoolerFilename) }} +

+

+ {{ singleBlockedMessage }} +

-
+

+ {{ batchBlockedMessage }} +

@@ -171,13 +220,20 @@
-
+

+ {{ batchBlockedMessage }} +

Batch progress
@@ -237,7 +293,10 @@ import { StartBatchConversionJobsRequest, StartConversionJobRequest, } from "@/app/core/net/api/request"; -import { ConversionJobResponse } from "@/app/core/net/api/response"; +import { + ConversionJobResponse, + ConversionToolchainStatusResponse, +} from "@/app/core/net/api/response"; import CoolerFileSelector from "./converter/CoolerFileSelector.vue"; import ConverterStatusChecker from "./converter/ConverterStatusChecker.vue"; @@ -270,6 +329,8 @@ const allFiles: Ref> = ref(new Set()); const lastSelectedIndex: Ref = ref(null); const overwriteConfirmVisible: Ref = ref(false); const overwriteConfirmMessage: Ref = ref(""); +const toolchainStatus: Ref = ref(null); +const toolchainLoading: Ref = ref(true); let overwriteConfirmResolver: ((approved: boolean) => void) | null = null; function cancelPendingOverwriteConfirm(): void { @@ -321,6 +382,8 @@ function resetState(): void { batchProgressMap.value.clear(); allFiles.value = new Set(); lastSelectedIndex.value = null; + toolchainStatus.value = null; + toolchainLoading.value = true; } } @@ -333,6 +396,21 @@ function onCoolerFileSelected(coolerFilename: string): void { selectedCoolerFilename.value = coolerFilename; } +function requiresHicToolchain(filename: string | null | undefined): boolean { + return filename?.toLowerCase().endsWith(".hic") ?? false; +} + +function deriveDirection(filename: string): string { + const lower = filename.toLowerCase(); + if (lower.endsWith(".hic")) { + return "hic-to-hict"; + } + if (lower.endsWith(".hict") || lower.endsWith(".hict.hdf5")) { + return "hict-to-mcool"; + } + return "mcool-to-hict"; +} + async function convertCooler(): Promise { const filename = selectedCoolerFilename.value; if (!filename) { @@ -353,7 +431,7 @@ async function convertCooler(): Promise { .startConversionJob( new StartConversionJobRequest({ filename: filename, - direction: "mcool-to-hict", + direction: deriveDirection(filename), overwrite: overwriteExisting, }) ) @@ -375,6 +453,7 @@ onMounted(() => { } mode.value = "batch"; batchStep.value = "select"; + loadToolchainStatus(); loadBatchFiles(); modal.value = new Modal(convertCoolerModal.value ?? "loadAGPModal", { backdrop: "static", @@ -408,7 +487,7 @@ function switchToBatch(): void { function loadBatchFiles(): void { Promise.all([ - props.networkManager.requestManager.listCoolers(), + props.networkManager.requestManager.listConvertibleMatrices(), props.networkManager.requestManager.listFiles(), ]) .then(([coolers, files]) => { @@ -428,6 +507,22 @@ function loadBatchFiles(): void { }); } +function loadToolchainStatus(): void { + toolchainLoading.value = true; + props.networkManager.requestManager + .getConversionToolchainStatus() + .then((status) => { + toolchainStatus.value = status; + }) + .catch((e) => { + errorMessage.value = e; + toolchainStatus.value = null; + }) + .finally(() => { + toolchainLoading.value = false; + }); +} + function isConverted(file: string): boolean { const output = deriveOutputFilename(file); return allFiles.value.has(output); @@ -435,6 +530,9 @@ function isConverted(file: string): boolean { function deriveOutputFilename(file: string): string { const lower = file.toLowerCase(); + if (lower.endsWith(".hic")) { + return file.slice(0, -".hic".length) + ".hict.hdf5"; + } if (lower.endsWith(".mcool")) { return file.slice(0, -".mcool".length) + ".hict.hdf5"; } @@ -576,6 +674,55 @@ const overallBatchStatusClass = computed(() => { return "running"; } }); + +const selectedRequiresHicToolchain = computed(() => + requiresHicToolchain(selectedCoolerFilename.value) +); + +const canConvertSelectedFile = computed(() => { + if (!selectedCoolerFilename.value) { + return false; + } + if (!selectedRequiresHicToolchain.value) { + return true; + } + return toolchainStatus.value?.hicConversionAvailable === true; +}); + +const singleBlockedMessage = computed(() => { + if (!selectedRequiresHicToolchain.value) { + return ""; + } + if (toolchainLoading.value) { + return "Inspecting .hic conversion toolchain..."; + } + if (toolchainStatus.value?.hicConversionAvailable) { + return ""; + } + return ( + toolchainStatus.value?.summary ?? + "No external .hic conversion toolchain is available in this build." + ); +}); + +const batchBlockedMessage = computed(() => { + const hasHicSelection = Array.from(batchSelection.value).some((file) => + requiresHicToolchain(file) + ); + if (!hasHicSelection) { + return ""; + } + if (toolchainLoading.value) { + return "Inspecting .hic conversion toolchain..."; + } + if (toolchainStatus.value?.hicConversionAvailable) { + return ""; + } + return ( + toolchainStatus.value?.summary ?? + "No external .hic conversion toolchain is available in this build." + ); +}); diff --git a/src/app/ui/components/upper_ribbon/converter/CoolerFileSelector.vue b/src/app/ui/components/upper_ribbon/converter/CoolerFileSelector.vue index ef51174..3c831a6 100644 --- a/src/app/ui/components/upper_ribbon/converter/CoolerFileSelector.vue +++ b/src/app/ui/components/upper_ribbon/converter/CoolerFileSelector.vue @@ -32,7 +32,7 @@ class="form-select form-select-lg mb-3" v-model="selectedCoolerFilename" > - + @@ -105,7 +105,7 @@ const chooseInitialFilename = ( onMounted(() => { props.networkManager.requestManager - .listCoolers() + .listConvertibleMatrices() .then((lst) => { filenames.value = lst; const initial = chooseInitialFilename(props.initialFilename, lst); From c04e9f1bcc13a3da89e7c7ccf607f67bb95e30a4 Mon Sep 17 00:00:00 2001 From: Alexander Serdyukov Date: Thu, 23 Apr 2026 00:47:38 +0400 Subject: [PATCH 2/6] Intermediate wizard + normalization implementations --- .../core/mapmanagers/CommonEventManager.ts | 4 + .../core/mapmanagers/VisualizationManager.ts | 154 +- src/app/core/net/api/RequestManager.ts | 87 + src/app/core/net/api/request.ts | 37 + src/app/core/net/api/response.ts | 42 + src/app/core/net/dto/dto.ts | 12 +- src/app/core/net/dto/requestDTO.ts | 48 +- src/app/core/net/dto/responseDTO.ts | 64 + .../visualization/VisualizationOptions.ts | 10 +- src/app/core/visualization/presetCatalog.ts | 271 +++ .../visualization/renderPipelineWizard.ts | 240 +++ src/app/stores/matrixViewStore.ts | 38 + src/app/stores/visualizationOptionsStore.ts | 16 +- src/app/ui/MainUIComponent.vue | 62 +- .../components/sidebar/SavedVisualOptions.vue | 18 +- .../upper_ribbon/FileWizardModal.vue | 1450 +++++++++++++++++ .../components/upper_ribbon/HeaderRibbon.vue | 23 +- .../components/upper_ribbon/NavigationBar.vue | 56 +- .../upper_ribbon/NormalizationSelector.vue | 123 +- .../upper_ribbon/RenderingPipelineModal.vue | 2 +- .../components/upper_ribbon/TrackManager.vue | 31 +- .../ui/components/upper_ribbon/UpperFrame.vue | 6 + 22 files changed, 2763 insertions(+), 31 deletions(-) create mode 100644 src/app/core/visualization/presetCatalog.ts create mode 100644 src/app/core/visualization/renderPipelineWizard.ts create mode 100644 src/app/stores/matrixViewStore.ts create mode 100644 src/app/ui/components/upper_ribbon/FileWizardModal.vue diff --git a/src/app/core/mapmanagers/CommonEventManager.ts b/src/app/core/mapmanagers/CommonEventManager.ts index 6e2d90f..ee3bad3 100644 --- a/src/app/core/mapmanagers/CommonEventManager.ts +++ b/src/app/core/mapmanagers/CommonEventManager.ts @@ -38,6 +38,7 @@ import { MoveSelectionToDebrisRequest, } from "../net/api/request"; import { ContactMapManager } from "./ContactMapManager"; +import { useMatrixViewStore } from "@/app/stores/matrixViewStore"; import { ActiveTool } from "./HiCViewAndLayersManager"; import { BorderStyle, NamePlacement } from "@/app/core/tracks/Track2DSymmetric"; import { Coordinate } from "ol/coordinate"; @@ -681,6 +682,7 @@ class CommonEventManager { } public onExportFASTAForSelectionClicked(): void { + const matrixViewStore = useMatrixViewStore(); this.mapManager.deactivateTranslocation(); const [fromPx, toPx] = [ this.mapManager.viewAndLayersManager.currentViewState.selectionBorders @@ -713,6 +715,8 @@ class CommonEventManager { fromBpY: fromBpY, toBpX: toBpX, toBpY: toBpY, + horizontalSource: matrixViewStore.horizontalFastaSource, + verticalSource: matrixViewStore.verticalFastaSource, }) ) .then((data) => { diff --git a/src/app/core/mapmanagers/VisualizationManager.ts b/src/app/core/mapmanagers/VisualizationManager.ts index ad8e230..8cd3b60 100644 --- a/src/app/core/mapmanagers/VisualizationManager.ts +++ b/src/app/core/mapmanagers/VisualizationManager.ts @@ -26,6 +26,40 @@ import { import { ContactMapManager } from "./ContactMapManager"; import { useVisualizationOptionsStore } from "@/app/stores/visualizationOptionsStore"; import VisualizationOptions from "../visualization/VisualizationOptions"; +import SimpleLinearGradient from "../visualization/colormap/SimpleLinearGradient"; + +type ViewportPixelBounds = { + bpResolution: number; + startRowPx: number; + endRowPx: number; + startColPx: number; + endColPx: number; +}; + +const clampQuantile = (value: number): number => { + if (!Number.isFinite(value)) { + return 0.995; + } + return Math.min(0.999999, Math.max(0.5, value)); +}; + +const computeFiniteQuantile = (values: Float32Array, quantile: number): number | null => { + const filtered: number[] = []; + for (const value of values) { + if (Number.isFinite(value) && value > 0) { + filtered.push(value); + } + } + if (filtered.length === 0) { + return null; + } + filtered.sort((left, right) => left - right); + const position = Math.min( + filtered.length - 1, + Math.max(0, Math.floor(clampQuantile(quantile) * (filtered.length - 1))) + ); + return filtered[position] ?? filtered[filtered.length - 1] ?? null; +}; class VisualizationManager { public static readonly VISUALIZATION_OPTIONS_UPDATED_EVENT = @@ -47,7 +81,105 @@ class VisualizationManager { }); } - public sendVisualizationOptionsToServer(): Promise { + private resolveViewportPixelBounds(): ViewportPixelBounds | null { + const size = this.mapManager.map.getSize(); + if (!size || size.length < 2 || size[0] <= 0 || size[1] <= 0) { + return null; + } + const descriptor = + this.mapManager.viewAndLayersManager.currentViewState.resolutionDesciptor; + if ( + !Number.isFinite(descriptor.bpResolution) || + !Number.isFinite(descriptor.pixelResolution) || + descriptor.pixelResolution <= 0 + ) { + return null; + } + const extent = this.mapManager.getView().calculateExtent(size); + const startColPx = Math.max( + 0, + Math.floor((extent[0] ?? 0) / descriptor.pixelResolution) + ); + const endColPx = Math.max( + startColPx + 1, + Math.ceil((extent[2] ?? 0) / descriptor.pixelResolution) + ); + const startRowPx = Math.max( + 0, + Math.floor(-(extent[3] ?? 0) / descriptor.pixelResolution) + ); + const endRowPx = Math.max( + startRowPx + 1, + Math.ceil(-(extent[1] ?? 0) / descriptor.pixelResolution) + ); + return { + bpResolution: descriptor.bpResolution, + startRowPx, + endRowPx, + startColPx, + endColPx, + }; + } + + public async syncAutoThresholdToViewport(): Promise { + const options = this.visualizationOptionsStore.asVisualizationOptions(); + if (!options.autoThresholdEnabled) { + return null; + } + if (!(options.colormap instanceof SimpleLinearGradient)) { + return null; + } + const bounds = this.resolveViewportPixelBounds(); + if (!bounds) { + return null; + } + const response = await this.mapManager.networkManager.requestManager.queryMatrixFloat32( + { + ...bounds, + signalMode: "TRADITIONAL_NORMALIZED", + } + ); + const nextUpperBound = computeFiniteQuantile( + response.values, + options.autoThresholdQuantile + ); + if ( + nextUpperBound == null || + !Number.isFinite(nextUpperBound) || + nextUpperBound <= options.colormap.minSignal + ) { + return null; + } + if (Math.abs(nextUpperBound - options.colormap.maxSignal) < 1e-9) { + return nextUpperBound; + } + this.visualizationOptionsStore.setVisualizationOptions( + new VisualizationOptions( + options.preLogBase, + options.postLogBase, + options.applyCoolerWeights, + options.resolutionScaling, + options.resolutionLinearScaling, + new SimpleLinearGradient( + options.colormap.startColorRGBA, + options.colormap.endColorRGBA, + options.colormap.minSignal, + nextUpperBound + ), + options.autoThresholdEnabled, + options.autoThresholdQuantile, + options.signalDisplayMode + ) + ); + return nextUpperBound; + } + + public async sendVisualizationOptionsToServer(options?: { + skipAutoThresholdRefresh?: boolean; + }): Promise { + if (!options?.skipAutoThresholdRefresh) { + await this.syncAutoThresholdToViewport().catch(() => null); + } return this.mapManager.networkManager.requestManager .setVisualizationOptions( new SetVisualizationOptionsRequest({ @@ -64,6 +196,26 @@ class VisualizationManager { return options; }); } + + public async sendVisualizationOptionsAndReload(options?: { + skipAutoThresholdRefresh?: boolean; + }): Promise { + const result = await this.sendVisualizationOptionsToServer(options); + this.mapManager.reloadTiles(); + return result; + } + + public async refreshAutoThresholdAndReload(): Promise { + const nextUpperBound = await this.syncAutoThresholdToViewport(); + if (nextUpperBound == null) { + return null; + } + await this.sendVisualizationOptionsToServer({ + skipAutoThresholdRefresh: true, + }); + this.mapManager.reloadTiles(); + return nextUpperBound; + } } export { VisualizationManager }; diff --git a/src/app/core/net/api/RequestManager.ts b/src/app/core/net/api/RequestManager.ts index bc63ad6..a87f58c 100644 --- a/src/app/core/net/api/RequestManager.ts +++ b/src/app/core/net/api/RequestManager.ts @@ -36,8 +36,10 @@ import { TracksPrecomputeStatusResponseDTO, TrackCompatibilityReportResponseDTO, FileEntryResponseDTO, + MatrixSourceResolutionResponseDTO, TrackFeatureContextResponseDTO, TrackFeatureSearchResponseDTO, + TrackPrecomputeCacheProbeResponseDTO, TrackQueryResponseDTO, TrackSummaryResponseDTO, WorkerSchedulerDiagnosticsResponseDTO, @@ -57,6 +59,8 @@ import { ListFilesDetailedRequest, ListFASTAFilesRequest, ListFilesRequest, + ResolveMatrixSourceRequest, + DropAllCachesRequest, LoadAGPRequest, MoveSelectionRangeRequest, OpenFileRequest, @@ -99,6 +103,7 @@ import { GetTrackFeatureContextRequest, StartTracksPrecomputeRequest, GetTracksPrecomputeStatusRequest, + ProbeTrackPrecomputeCacheRequest, GetWorkerDiagnosticsRequest, GetRenderPipelineRequest, SetRenderPipelineRequest, @@ -110,10 +115,12 @@ import { CurrentSignalRangeResponse, FastaLinkResponse, FileEntryResponse, + MatrixSourceResolutionResponse, NameMappingResponse, TrackCompatibilityReportResponse, TrackFeatureContextResponse, TrackFeatureSearchResponse, + TrackPrecomputeCacheProbeResponse, TracksPrecomputeStatusResponse, TrackQueryResponse, TrackSummaryResponse, @@ -414,6 +421,28 @@ class RequestManager { return response.data as string[]; } + public async resolveMatrixSource( + filename: string + ): Promise { + return this.sendRequest(new ResolveMatrixSourceRequest({ filename })) + .then((response) => response.data) + .then((json) => new MatrixSourceResolutionResponseDTO(json).toEntity()); + } + + public async dropAllCaches(): Promise<{ + status: string; + matrixMetadataDeleted: number; + trackCacheEntriesDeleted: number; + }> { + return this.sendRequest(new DropAllCachesRequest()) + .then((response) => response.data as Record) + .then((json) => ({ + status: String(json.status ?? "unknown"), + matrixMetadataDeleted: Number(json.matrixMetadataDeleted ?? 0), + trackCacheEntriesDeleted: Number(json.trackCacheEntriesDeleted ?? 0), + })); + } + public async openTrack( filename: string, name?: string, @@ -621,6 +650,16 @@ class RequestManager { .then((json) => new TracksPrecomputeStatusResponseDTO(json).toEntity()); } + public async probeTrackPrecomputeCache( + filename: string + ): Promise { + return this.sendRequest(new ProbeTrackPrecomputeCacheRequest({ filename })) + .then((response) => response.data) + .then((json) => + new TrackPrecomputeCacheProbeResponseDTO(json).toEntity() + ); + } + public async getWorkerDiagnostics(): Promise { return this.sendRequest(new GetWorkerDiagnosticsRequest()) .then((response) => response.data) @@ -763,6 +802,54 @@ class RequestManager { .catch(() => "unknown"); } + public async queryMatrixFloat32(options: { + bpResolution: number; + startRowPx: number; + endRowPx: number; + startColPx: number; + endColPx: number; + signalMode?: "RAW_COUNTS" | "COOLER_WEIGHTED" | "TRADITIONAL_NORMALIZED" | "PIPELINE_SIGNAL"; + }): Promise<{ + rows: number; + cols: number; + values: Float32Array; + }> { + const host = this.networkManager.host.replace(/\/+$/, ""); + const response = await axios.post( + `${host}/matrix/query`, + { + unit: "PIXELS", + bpResolution: options.bpResolution, + startRowPx: options.startRowPx, + endRowPx: options.endRowPx, + startColPx: options.startColPx, + endColPx: options.endColPx, + signalMode: options.signalMode ?? "TRADITIONAL_NORMALIZED", + format: "BINARY_FLOAT32", + }, + { + responseType: "arraybuffer", + headers: { + Accept: "application/octet-stream", + }, + } + ); + const rows = Number.parseInt(response.headers["x-hict-rows"] || "0", 10); + const cols = Number.parseInt(response.headers["x-hict-cols"] || "0", 10); + const buffer = response.data as ArrayBuffer; + const count = Math.max(0, Math.floor(buffer.byteLength / 4)); + const view = new DataView(buffer); + const values = new Float32Array(count); + for (let index = 0; index < count; index += 1) { + values[index] = view.getFloat32(index * 4, true); + } + return { + rows, + cols, + values, + }; + } + public async listAGPFiles(): Promise { const response = await this.sendRequest(new ListAGPFilesRequest()); return response.data as string[]; diff --git a/src/app/core/net/api/request.ts b/src/app/core/net/api/request.ts index b482460..45775e6 100644 --- a/src/app/core/net/api/request.ts +++ b/src/app/core/net/api/request.ts @@ -81,6 +81,20 @@ class ListTrackFilesRequest implements HiCTAPIRequest { requestPath = "/tracks/list_files"; } +class ResolveMatrixSourceRequest implements HiCTAPIRequest { + requestPath = "/resolve_matrix_source"; + + public constructor( + public readonly options: { + readonly filename: string; + } + ) {} +} + +class DropAllCachesRequest implements HiCTAPIRequest { + requestPath = "/cache/drop_all"; +} + class CloseFileRequest implements HiCTAPIRequest { requestPath = "/close"; } @@ -91,6 +105,12 @@ class AttachSessionRequest implements HiCTAPIRequest { class GetFastaForAssemblyRequest implements HiCTAPIRequest { requestPath = "/get_fasta_for_assembly"; + + public constructor( + public readonly options: { + readonly source?: "PRIMARY" | "SECONDARY"; + } = {} + ) {} } class GetAGPForAssemblyRequest implements HiCTAPIRequest { @@ -302,6 +322,8 @@ class GetFastaForSelectionRequest implements HiCTAPIRequest { readonly fromBpY: number; readonly toBpX: number; readonly toBpY: number; + readonly horizontalSource?: "PRIMARY" | "SECONDARY"; + readonly verticalSource?: "PRIMARY" | "SECONDARY"; } ) {} } @@ -313,6 +335,7 @@ class LinkFASTARequest implements HiCTAPIRequest { public readonly options: { readonly fastaFilename: string; readonly allowMismatch?: boolean; + readonly source?: "PRIMARY" | "SECONDARY"; } ) {} } @@ -323,6 +346,7 @@ class LoadAGPRequest implements HiCTAPIRequest { public constructor( public readonly options: { readonly agpFilename: string; + readonly source?: "PRIMARY" | "SECONDARY"; } ) {} } @@ -536,6 +560,16 @@ class GetTracksPrecomputeStatusRequest implements HiCTAPIRequest { requestPath = "/tracks/precompute/status"; } +class ProbeTrackPrecomputeCacheRequest implements HiCTAPIRequest { + requestPath = "/tracks/precompute/probe"; + + public constructor( + public readonly options: { + readonly filename: string; + } + ) {} +} + // class TileLoadPOSTRequest implements HiCTAPIRequest { // requestPath = "/get_tile"; @@ -555,6 +589,8 @@ export { CloseFileRequest, ListCoolerFilesRequest, ListConvertibleMatrixFilesRequest, + ResolveMatrixSourceRequest, + DropAllCachesRequest, StartConversionJobRequest, StartBatchConversionJobsRequest, ListConversionJobsRequest, @@ -607,6 +643,7 @@ export { GetTrackFeatureContextRequest, StartTracksPrecomputeRequest, GetTracksPrecomputeStatusRequest, + ProbeTrackPrecomputeCacheRequest, GetWorkerDiagnosticsRequest, GetRenderPipelineRequest, SetRenderPipelineRequest, diff --git a/src/app/core/net/api/response.ts b/src/app/core/net/api/response.ts index dc5cbf1..892494e 100644 --- a/src/app/core/net/api/response.ts +++ b/src/app/core/net/api/response.ts @@ -251,6 +251,45 @@ class FileEntryResponse { ) {} } +class FileFingerprintResponse { + public constructor( + public readonly sizeBytes: number, + public readonly modifiedAtMs: number, + public readonly sha256: string, + public readonly sha512: string + ) {} +} + +class MatrixSourceResolutionResponse { + public constructor( + public readonly inputFilename: string, + public readonly inputKind: string, + public readonly action: string, + public readonly resolvedFilename: string, + public readonly expectedOutputFilename: string | null, + public readonly conversionDirection: string | null, + public readonly cachedOutputExists: boolean, + public readonly cacheCurrent: boolean, + public readonly warnings: string[], + public readonly sourceFingerprint: FileFingerprintResponse | null, + public readonly outputFingerprint: FileFingerprintResponse | null + ) {} +} + +class TrackPrecomputeCacheProbeResponse { + public constructor( + public readonly filename: string, + public readonly trackType: string, + public readonly supported: boolean, + public readonly cacheAvailable: boolean, + public readonly cacheCurrent: boolean, + public readonly cacheSidecarPath: string, + public readonly warnings: string[], + public readonly sourceFingerprint: FileFingerprintResponse | null, + public readonly hictFingerprint: FileFingerprintResponse + ) {} +} + class WorkerPoolDiagnosticsResponse { public constructor( public readonly corePoolSize: number, @@ -342,6 +381,9 @@ export { TracksPrecomputeStatusResponse, TrackCompatibilityReportResponse, FileEntryResponse, + FileFingerprintResponse, + MatrixSourceResolutionResponse, + TrackPrecomputeCacheProbeResponse, WorkerPoolDiagnosticsResponse, WorkerCancellationDomainDiagnosticsResponse, WorkerSchedulerDiagnosticsResponse, diff --git a/src/app/core/net/dto/dto.ts b/src/app/core/net/dto/dto.ts index 2bbddc5..66c9708 100644 --- a/src/app/core/net/dto/dto.ts +++ b/src/app/core/net/dto/dto.ts @@ -251,6 +251,9 @@ class VisualizationOptionsDTO extends InboundDTO { applyCoolerWeights: e.applyCoolerWeights, resolutionScaling: e.resolutionScaling, resolutionLinearScaling: e.resolutionLinearScaling, + autoThresholdEnabled: e.autoThresholdEnabled, + autoThresholdQuantile: e.autoThresholdQuantile, + signalDisplayMode: e.signalDisplayMode, colormap: ColormapDTO.fromEntity(e.colormap), }); } @@ -265,7 +268,14 @@ class VisualizationOptionsDTO extends InboundDTO { this.json["resolutionLinearScaling"] as boolean, new ColormapDTO( this.json["colormap"] as Record - ).toEntity() + ).toEntity(), + Boolean(this.json["autoThresholdEnabled"] ?? false), + typeof this.json["autoThresholdQuantile"] === "number" + ? (this.json["autoThresholdQuantile"] as number) + : 0.995, + typeof this.json["signalDisplayMode"] === "string" + ? (this.json["signalDisplayMode"] as VisualizationOptions["signalDisplayMode"]) + : "OBSERVED" ); } } diff --git a/src/app/core/net/dto/requestDTO.ts b/src/app/core/net/dto/requestDTO.ts index 608ecbc..b11fb07 100644 --- a/src/app/core/net/dto/requestDTO.ts +++ b/src/app/core/net/dto/requestDTO.ts @@ -52,6 +52,8 @@ import { GetAGPForAssemblyRequest, ListCoolerFilesRequest, ListTrackFilesRequest, + ResolveMatrixSourceRequest, + DropAllCachesRequest, OpenTrackRequest, OpenCoolerWeightsTrackRequest, ProbeTrackCompatibilityRequest, @@ -64,6 +66,7 @@ import { GetTrackFeatureContextRequest, StartTracksPrecomputeRequest, GetTracksPrecomputeStatusRequest, + ProbeTrackPrecomputeCacheRequest, StartConversionJobRequest, StartBatchConversionJobsRequest, ListConversionJobsRequest, @@ -147,6 +150,12 @@ abstract class HiCTAPIRequestDTO< return new ListCoolerFilesRequestDTO(entity); case entity instanceof ListTrackFilesRequest: return new ListTrackFilesRequestDTO(entity); + case entity instanceof ResolveMatrixSourceRequest: + return new ResolveMatrixSourceRequestDTO( + entity as ResolveMatrixSourceRequest + ); + case entity instanceof DropAllCachesRequest: + return new DropAllCachesRequestDTO(entity as DropAllCachesRequest); case entity instanceof OpenTrackRequest: return new OpenTrackRequestDTO(entity as OpenTrackRequest); case entity instanceof OpenCoolerWeightsTrackRequest: @@ -177,6 +186,10 @@ abstract class HiCTAPIRequestDTO< return new StartTracksPrecomputeRequestDTO(entity as StartTracksPrecomputeRequest); case entity instanceof GetTracksPrecomputeStatusRequest: return new GetTracksPrecomputeStatusRequestDTO(entity as GetTracksPrecomputeStatusRequest); + case entity instanceof ProbeTrackPrecomputeCacheRequest: + return new ProbeTrackPrecomputeCacheRequestDTO( + entity as ProbeTrackPrecomputeCacheRequest + ); case entity instanceof ListConversionJobsRequest: return new ListConversionJobsRequestDTO(entity); case entity instanceof GetConversionJobRequest: @@ -516,6 +529,7 @@ class LinkFASTARequestDTO extends HiCTAPIRequestDTO { return { fastaFilename: this.entity.options.fastaFilename, allowMismatch: this.entity.options.allowMismatch, + source: this.entity.options.source, }; } } @@ -523,6 +537,7 @@ class LoadAGPRequestDTO extends HiCTAPIRequestDTO { toDTO(): Record { return { agpFilename: this.entity.options.agpFilename, + source: this.entity.options.source, }; } } @@ -604,6 +619,20 @@ class ListTrackFilesRequestDTO extends HiCTAPIRequestDTO } } +class ResolveMatrixSourceRequestDTO extends HiCTAPIRequestDTO { + toDTO(): Record { + return { + filename: this.entity.options.filename, + }; + } +} + +class DropAllCachesRequestDTO extends HiCTAPIRequestDTO { + toDTO(): Record { + return {}; + } +} + class OpenTrackRequestDTO extends HiCTAPIRequestDTO { toDTO(): Record { return { @@ -757,6 +786,14 @@ class GetTracksPrecomputeStatusRequestDTO extends HiCTAPIRequestDTO { + toDTO(): Record { + return { + filename: this.entity.options.filename, + }; + } +} + class ListFASTAFilesRequestDTO extends HiCTAPIRequestDTO { toDTO(): Record { return {}; @@ -782,10 +819,12 @@ class AttachSessionRequestDTO extends HiCTAPIRequestDTO { class GetFastaForAssemblyRequestDTO extends HiCTAPIRequestDTO { toDTO(): Record { - return {}; + return { + source: this.entity.options.source, + }; } } -class GetAGPForAssemblyRequestDTO extends HiCTAPIRequestDTO { +class GetAGPForAssemblyRequestDTO extends HiCTAPIRequestDTO { toDTO(): Record { return {}; } @@ -798,6 +837,8 @@ class GetFastaForSelectionRequestDTO extends HiCTAPIRequestDTO { } } +class FileFingerprintResponseDTO extends InboundDTO { + public toEntity(): FileFingerprintResponse { + return new FileFingerprintResponse( + (this.json["sizeBytes"] as number) ?? -1, + (this.json["modifiedAtMs"] as number) ?? 0, + (this.json["sha256"] as string) ?? "", + (this.json["sha512"] as string) ?? "" + ); + } +} + +class MatrixSourceResolutionResponseDTO extends InboundDTO { + public toEntity(): MatrixSourceResolutionResponse { + return new MatrixSourceResolutionResponse( + (this.json["inputFilename"] as string) ?? "", + (this.json["inputKind"] as string) ?? "UNKNOWN", + (this.json["action"] as string) ?? "UNSUPPORTED", + (this.json["resolvedFilename"] as string) ?? "", + (this.json["expectedOutputFilename"] as string) ?? null, + (this.json["conversionDirection"] as string) ?? null, + Boolean(this.json["cachedOutputExists"] ?? false), + Boolean(this.json["cacheCurrent"] ?? false), + (this.json["warnings"] as string[]) ?? [], + this.json["sourceFingerprint"] + ? new FileFingerprintResponseDTO( + this.json["sourceFingerprint"] as Record + ).toEntity() + : null, + this.json["outputFingerprint"] + ? new FileFingerprintResponseDTO( + this.json["outputFingerprint"] as Record + ).toEntity() + : null + ); + } +} + +class TrackPrecomputeCacheProbeResponseDTO extends InboundDTO { + public toEntity(): TrackPrecomputeCacheProbeResponse { + return new TrackPrecomputeCacheProbeResponse( + (this.json["filename"] as string) ?? "", + (this.json["trackType"] as string) ?? "UNSUPPORTED", + Boolean(this.json["supported"] ?? false), + Boolean(this.json["cacheAvailable"] ?? false), + Boolean(this.json["cacheCurrent"] ?? false), + (this.json["cacheSidecarPath"] as string) ?? "", + (this.json["warnings"] as string[]) ?? [], + this.json["sourceFingerprint"] + ? new FileFingerprintResponseDTO( + this.json["sourceFingerprint"] as Record + ).toEntity() + : null, + new FileFingerprintResponseDTO( + (this.json["hictFingerprint"] as Record) ?? {} + ).toEntity() + ); + } +} + class WorkerPoolDiagnosticsResponseDTO extends InboundDTO { public toEntity(): WorkerPoolDiagnosticsResponse { return new WorkerPoolDiagnosticsResponse( @@ -460,6 +522,8 @@ export { TracksPrecomputeStatusResponseDTO, TrackCompatibilityReportResponseDTO, FileEntryResponseDTO, + MatrixSourceResolutionResponseDTO, + TrackPrecomputeCacheProbeResponseDTO, WorkerSchedulerDiagnosticsResponseDTO, FastaLinkResponseDTO, }; diff --git a/src/app/core/visualization/VisualizationOptions.ts b/src/app/core/visualization/VisualizationOptions.ts index 8875279..de94f8e 100644 --- a/src/app/core/visualization/VisualizationOptions.ts +++ b/src/app/core/visualization/VisualizationOptions.ts @@ -21,6 +21,11 @@ import Colormap from "./colormap/Colormap"; +export type SignalDisplayMode = + | "OBSERVED" + | "EXPECTED" + | "OBSERVED_OVER_EXPECTED"; + export default class VisualizationOptions { public constructor( public readonly preLogBase: number, @@ -28,6 +33,9 @@ export default class VisualizationOptions { public readonly applyCoolerWeights: boolean | undefined, public readonly resolutionScaling: boolean | undefined, public readonly resolutionLinearScaling: boolean | undefined, - public readonly colormap: Colormap + public readonly colormap: Colormap, + public readonly autoThresholdEnabled: boolean = false, + public readonly autoThresholdQuantile: number = 0.995, + public readonly signalDisplayMode: SignalDisplayMode = "OBSERVED" ) {} } diff --git a/src/app/core/visualization/presetCatalog.ts b/src/app/core/visualization/presetCatalog.ts new file mode 100644 index 0000000..2619eff --- /dev/null +++ b/src/app/core/visualization/presetCatalog.ts @@ -0,0 +1,271 @@ +/* + Copyright (c) 2021-2026 Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis, Zakhar Lobanov, Nikita Zheleznov and Computer Technologies Laboratory ITMO University team. + + Permission is hereby granted, free of charge, to any person obtaining a copy of + this software and associated documentation files (the "Software"), to deal in + the Software without restriction, including without limitation the rights to + use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of + the Software, and to permit persons to whom the Software is furnished to do so, + subject to the following conditions: + + The above copyright notice and this permission notice shall be included in all + copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS + FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR + COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER + IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN + CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. + */ + +import type { TrackStylePresetBundle } from "@/app/core/tracks/TrackStylePreset"; +import defaultOptions from "@/app/core/visualization/colormap/default_options.json"; +import type { SessionVisualizationPreset } from "@/app/stores/sessionStore"; +import VisualizationOptions from "./VisualizationOptions"; +import Colormap from "./colormap/Colormap"; +import SimpleLinearGradient from "./colormap/SimpleLinearGradient"; +import { ColorTranslator } from "colortranslator"; + +export type VisualizationPresetRecord = { + option_id: number; + name: string; + options: VisualizationOptions; + backgroundColor: string; + trackStyles?: TrackStylePresetBundle; + signalThresholds?: { + lowerSignalBound?: number; + upperSignalBound?: number; + }; + origin: "builtin" | "session"; +}; + +type UnknownRecord = Record; + +const isRecord = (value: unknown): value is UnknownRecord => + typeof value === "object" && value !== null; + +const safeColor = (value: unknown, fallback: string): ColorTranslator => { + if (typeof value !== "string" || value.length > 128) { + return new ColorTranslator(fallback, { legacyCSS: true }); + } + try { + return new ColorTranslator(value, { legacyCSS: true }); + } catch { + return new ColorTranslator(fallback, { legacyCSS: true }); + } +}; + +export const serializeVisualizationOptions = ( + options: VisualizationOptions +): Record => { + const cmap = options.colormap; + if (cmap instanceof SimpleLinearGradient) { + return { + preLogBase: options.preLogBase, + postLogBase: options.postLogBase, + applyCoolerWeights: options.applyCoolerWeights ?? false, + resolutionScaling: options.resolutionScaling ?? false, + resolutionLinearScaling: options.resolutionLinearScaling ?? false, + autoThresholdEnabled: options.autoThresholdEnabled ?? false, + autoThresholdQuantile: options.autoThresholdQuantile ?? 0.995, + signalDisplayMode: options.signalDisplayMode ?? "OBSERVED", + colormap: { + colormapType: cmap.colormapType, + startColorRGBAString: cmap.startColorRGBA.RGBA, + endColorRGBAString: cmap.endColorRGBA.RGBA, + minSignal: cmap.minSignal, + maxSignal: cmap.maxSignal, + }, + }; + } + return { + preLogBase: options.preLogBase, + postLogBase: options.postLogBase, + applyCoolerWeights: options.applyCoolerWeights ?? false, + resolutionScaling: options.resolutionScaling ?? false, + resolutionLinearScaling: options.resolutionLinearScaling ?? false, + autoThresholdEnabled: options.autoThresholdEnabled ?? false, + autoThresholdQuantile: options.autoThresholdQuantile ?? 0.995, + signalDisplayMode: options.signalDisplayMode ?? "OBSERVED", + colormap: { + colormapType: options.colormap?.colormapType ?? "Unknown", + }, + }; +}; + +export const deserializeVisualizationOptions = ( + raw: Record +): VisualizationOptions => { + const preLogBase = typeof raw.preLogBase === "number" ? raw.preLogBase : -1; + const postLogBase = + typeof raw.postLogBase === "number" ? raw.postLogBase : 10; + const applyCoolerWeights = + typeof raw.applyCoolerWeights === "boolean" + ? raw.applyCoolerWeights + : false; + const resolutionScaling = + typeof raw.resolutionScaling === "boolean" ? raw.resolutionScaling : false; + const resolutionLinearScaling = + typeof raw.resolutionLinearScaling === "boolean" + ? raw.resolutionLinearScaling + : false; + const autoThresholdEnabled = + typeof raw.autoThresholdEnabled === "boolean" + ? raw.autoThresholdEnabled + : false; + const autoThresholdQuantile = + typeof raw.autoThresholdQuantile === "number" && + Number.isFinite(raw.autoThresholdQuantile) + ? raw.autoThresholdQuantile + : 0.995; + const signalDisplayMode = + raw.signalDisplayMode === "EXPECTED" || + raw.signalDisplayMode === "OBSERVED_OVER_EXPECTED" + ? raw.signalDisplayMode + : "OBSERVED"; + const cmapRaw = isRecord(raw.colormap) ? raw.colormap : {}; + const cmapType = + typeof cmapRaw.colormapType === "string" + ? cmapRaw.colormapType + : "Unknown"; + let cmap: Colormap; + if (cmapType === "SimpleLinearGradient") { + const startColor = + typeof cmapRaw.startColorRGBAString === "string" + ? cmapRaw.startColorRGBAString + : "rgba(0,255,0,0.0)"; + const endColor = + typeof cmapRaw.endColorRGBAString === "string" + ? cmapRaw.endColorRGBAString + : "rgba(0,96,0,1.0)"; + const minSignal = + typeof cmapRaw.minSignal === "number" ? cmapRaw.minSignal : 0; + const maxSignal = + typeof cmapRaw.maxSignal === "number" ? cmapRaw.maxSignal : 1; + cmap = new SimpleLinearGradient( + safeColor(startColor, "rgba(0,255,0,0.0)"), + safeColor(endColor, "rgba(0,96,0,1.0)"), + minSignal, + maxSignal + ); + } else { + cmap = new Colormap(cmapType); + } + return new VisualizationOptions( + preLogBase, + postLogBase, + applyCoolerWeights, + resolutionScaling, + resolutionLinearScaling, + cmap, + autoThresholdEnabled, + autoThresholdQuantile, + signalDisplayMode + ); +}; + +export const getVisualizationSignalThresholds = ( + options: VisualizationOptions +): { + lowerSignalBound?: number; + upperSignalBound?: number; +} => { + const cmap = options.colormap; + if (cmap instanceof SimpleLinearGradient) { + return { + lowerSignalBound: cmap.minSignal, + upperSignalBound: cmap.maxSignal, + }; + } + return {}; +}; + +const toPresetRecord = ( + option: { + option_id?: number; + name?: string; + options?: Record; + backgroundColor?: string; + trackStyles?: TrackStylePresetBundle; + signalThresholds?: { + lowerSignalBound?: number; + upperSignalBound?: number; + }; + }, + optionId: number, + origin: "builtin" | "session" +): VisualizationPresetRecord => ({ + option_id: option.option_id ?? optionId, + name: option.name ?? `Preset ${optionId}`, + options: deserializeVisualizationOptions(option.options ?? {}), + backgroundColor: option.backgroundColor ?? "rgba(255,255,255,1.0)", + trackStyles: option.trackStyles, + signalThresholds: + option.signalThresholds ?? + getVisualizationSignalThresholds( + deserializeVisualizationOptions(option.options ?? {}) + ), + origin, +}); + +const extractBuiltinPresetRows = (): Array<{ + option_id?: number; + name?: string; + options?: Record; + backgroundColor?: string; + trackStyles?: TrackStylePresetBundle; + signalThresholds?: { + lowerSignalBound?: number; + upperSignalBound?: number; + }; +}> => { + const data = isRecord(defaultOptions) + ? ((defaultOptions as UnknownRecord).data as UnknownRecord | undefined) + : undefined; + if (!data) { + return []; + } + const source = Array.isArray(data.savedVisualizationPresets) + ? data.savedVisualizationPresets + : Array.isArray(data.savedLocations) + ? data.savedLocations + : []; + return source.filter(isRecord) as Array<{ + option_id?: number; + name?: string; + options?: Record; + backgroundColor?: string; + trackStyles?: TrackStylePresetBundle; + signalThresholds?: { + lowerSignalBound?: number; + upperSignalBound?: number; + }; + }>; +}; + +export const loadBuiltinVisualizationPresets = (): VisualizationPresetRecord[] => + extractBuiltinPresetRows().map((option, index) => + toPresetRecord(option, index, "builtin") + ); + +export const mergeVisualizationPresets = ( + sessionPresets: SessionVisualizationPreset[] +): VisualizationPresetRecord[] => { + const builtins = loadBuiltinVisualizationPresets(); + const session = sessionPresets.map((preset, index) => + toPresetRecord( + { + option_id: preset.option_id ?? index, + name: preset.name, + options: preset.options, + backgroundColor: preset.backgroundColor, + trackStyles: preset.trackStyles as TrackStylePresetBundle | undefined, + signalThresholds: preset.signalThresholds, + }, + index, + "session" + ) + ); + return [...builtins, ...session]; +}; diff --git a/src/app/core/visualization/renderPipelineWizard.ts b/src/app/core/visualization/renderPipelineWizard.ts new file mode 100644 index 0000000..2fe8c3b --- /dev/null +++ b/src/app/core/visualization/renderPipelineWizard.ts @@ -0,0 +1,240 @@ +/* + Copyright (c) 2021-2026 Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis, Zakhar Lobanov, Nikita Zheleznov and Computer Technologies Laboratory ITMO University team. + + Permission is hereby granted, free of charge, to any person obtaining a copy of + this software and associated documentation files (the "Software"), to deal in + the Software without restriction, including without limitation the rights to + use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of + the Software, and to permit persons to whom the Software is furnished to do so, + subject to the following conditions: + + The above copyright notice and this permission notice shall be included in all + copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS + FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR + COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER + IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN + CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. + */ + +import SimpleLinearGradient from "@/app/core/visualization/colormap/SimpleLinearGradient"; +import VisualizationOptions from "@/app/core/visualization/VisualizationOptions"; + +export type WizardViewMode = "single" | "overlay" | "split"; +export type WizardBlendMode = + | "OVER" + | "ADD" + | "SUBTRACT" + | "MULTIPLY" + | "SCREEN" + | "DIFFERENCE" + | "LIGHTEN" + | "DARKEN" + | "XOR"; + +type SourceName = "PRIMARY" | "SECONDARY"; +type TrackAxis = "ROW" | "COL"; + +type PipelineExpression = + | { type: "source"; source: SourceName } + | { type: "track1d"; trackId: string; axis: TrackAxis } + | { + type: "dynamic"; + field: "RESOLUTION_SCALING_COEFF" | "RESOLUTION_LINEAR_SCALING_COEFF"; + } + | { type: "log"; input: PipelineExpression; base: number } + | { + type: "binary"; + op: "MUL"; + left: PipelineExpression; + right: PipelineExpression; + } + | { + type: "colormap"; + mode: "LINEAR"; + input: PipelineExpression; + startColor: string; + endColor: string; + minSignal: number; + maxSignal: number; + } + | { + type: "pixel_blend"; + mode: WizardBlendMode; + top: PipelineExpression; + bottom: PipelineExpression; + topOpacity: number; + bottomOpacity: number; + }; + +const BUILTIN_COOLER_WEIGHTS_TRACK_ID = "__builtin_cooler_weights__"; + +const cloneExpression = (value: T): T => + JSON.parse(JSON.stringify(value)) as T; + +const safeHexa = (value: string, fallback: string): string => { + const normalized = String(value ?? fallback).trim().toLowerCase(); + if (/^#[0-9a-f]{8}$/.test(normalized)) { + return normalized; + } + if (/^#[0-9a-f]{6}$/.test(normalized)) { + return `${normalized}ff`; + } + return fallback; +}; + +const buildSignalExpression = ( + source: SourceName, + options: VisualizationOptions +): PipelineExpression => { + let expression: PipelineExpression = { + type: "source", + source, + }; + if ( + Number.isFinite(options.preLogBase) && + options.preLogBase > 0 && + Math.abs(options.preLogBase - 1) > 1e-9 + ) { + expression = { + type: "log", + input: expression, + base: options.preLogBase, + }; + } + if (options.resolutionScaling) { + expression = { + type: "binary", + op: "MUL", + left: expression, + right: { + type: "dynamic", + field: "RESOLUTION_SCALING_COEFF", + }, + }; + } + if (options.resolutionLinearScaling) { + expression = { + type: "binary", + op: "MUL", + left: expression, + right: { + type: "dynamic", + field: "RESOLUTION_LINEAR_SCALING_COEFF", + }, + }; + } + if (options.applyCoolerWeights) { + expression = { + type: "binary", + op: "MUL", + left: expression, + right: { + type: "binary", + op: "MUL", + left: { + type: "track1d", + trackId: BUILTIN_COOLER_WEIGHTS_TRACK_ID, + axis: "ROW", + }, + right: { + type: "track1d", + trackId: BUILTIN_COOLER_WEIGHTS_TRACK_ID, + axis: "COL", + }, + }, + }; + } + if ( + Number.isFinite(options.postLogBase) && + options.postLogBase > 0 && + Math.abs(options.postLogBase - 1) > 1e-9 + ) { + expression = { + type: "log", + input: expression, + base: options.postLogBase, + }; + } + return expression; +}; + +const buildColorExpression = ( + source: SourceName, + options: VisualizationOptions +): PipelineExpression => { + const gradient = options.colormap; + const linearGradient = + gradient instanceof SimpleLinearGradient ? gradient : undefined; + return { + type: "colormap", + mode: "LINEAR", + input: buildSignalExpression(source, options), + startColor: safeHexa( + linearGradient?.startColorRGBA?.HEXA ?? "#ffffff00", + "#ffffff00" + ), + endColor: safeHexa( + linearGradient?.endColorRGBA?.HEXA ?? "#006000ff", + "#006000ff" + ), + minSignal: + typeof linearGradient?.minSignal === "number" + ? linearGradient.minSignal + : 0, + maxSignal: + typeof linearGradient?.maxSignal === "number" + ? linearGradient.maxSignal + : 1, + }; +}; + +export const buildWizardRenderPipelineConfig = (options: { + viewMode: WizardViewMode; + primaryOptions: VisualizationOptions; + secondaryOptions?: VisualizationOptions; + blendMode?: WizardBlendMode; + topOpacity?: number; + bottomOpacity?: number; +}): Record => { + const primary = buildColorExpression("PRIMARY", options.primaryOptions); + if (options.viewMode === "single" || !options.secondaryOptions) { + return { + enabled: true, + swapUpperLower: false, + upperExpression: primary, + lowerExpression: cloneExpression(primary), + }; + } + + const secondary = buildColorExpression("SECONDARY", options.secondaryOptions); + if (options.viewMode === "overlay") { + const overlay: PipelineExpression = { + type: "pixel_blend", + mode: options.blendMode ?? "OVER", + top: primary, + bottom: secondary, + topOpacity: + typeof options.topOpacity === "number" ? options.topOpacity : 0.75, + bottomOpacity: + typeof options.bottomOpacity === "number" + ? options.bottomOpacity + : 1.0, + }; + return { + enabled: true, + swapUpperLower: false, + upperExpression: overlay, + lowerExpression: cloneExpression(overlay), + }; + } + + return { + enabled: true, + swapUpperLower: false, + upperExpression: primary, + lowerExpression: secondary, + }; +}; diff --git a/src/app/stores/matrixViewStore.ts b/src/app/stores/matrixViewStore.ts new file mode 100644 index 0000000..029daef --- /dev/null +++ b/src/app/stores/matrixViewStore.ts @@ -0,0 +1,38 @@ +import { defineStore } from "pinia"; +import { ref } from "vue"; + +export type MatrixPresentationMode = "single" | "overlay" | "split"; +export type MatrixSourceName = "PRIMARY" | "SECONDARY"; + +export const useMatrixViewStore = defineStore("matrixViewStore", () => { + const presentationMode = ref("single"); + const horizontalFastaSource = ref("PRIMARY"); + const verticalFastaSource = ref("PRIMARY"); + + function setPresentationMode(mode: MatrixPresentationMode) { + presentationMode.value = mode; + } + + function setSelectionFastaSources( + horizontal: MatrixSourceName, + vertical: MatrixSourceName + ) { + horizontalFastaSource.value = horizontal; + verticalFastaSource.value = vertical; + } + + function reset() { + presentationMode.value = "single"; + horizontalFastaSource.value = "PRIMARY"; + verticalFastaSource.value = "PRIMARY"; + } + + return { + presentationMode, + horizontalFastaSource, + verticalFastaSource, + setPresentationMode, + setSelectionFastaSources, + reset, + }; +}); diff --git a/src/app/stores/visualizationOptionsStore.ts b/src/app/stores/visualizationOptionsStore.ts index 40c45cc..2669dd6 100644 --- a/src/app/stores/visualizationOptionsStore.ts +++ b/src/app/stores/visualizationOptionsStore.ts @@ -34,6 +34,11 @@ export const useVisualizationOptionsStore = defineStore( const resolutionScaling = ref(false); const resolutionLinearScaling = ref(false); const postLogBase = ref(10); + const autoThresholdEnabled = ref(false); + const autoThresholdQuantile = ref(0.995); + const signalDisplayMode = ref( + "OBSERVED" + ); const colormap: Ref = ref( new SimpleLinearGradient( new ColorTranslator("rgba(0,255,0,0.0)", { legacyCSS: true }), @@ -50,7 +55,10 @@ export const useVisualizationOptionsStore = defineStore( applyCoolerWeights.value, resolutionScaling.value, resolutionLinearScaling.value, - colormap.value + colormap.value, + autoThresholdEnabled.value, + autoThresholdQuantile.value, + signalDisplayMode.value ); } @@ -60,6 +68,9 @@ export const useVisualizationOptionsStore = defineStore( applyCoolerWeights.value = options.applyCoolerWeights ?? false; resolutionScaling.value = options.resolutionScaling ?? false; resolutionLinearScaling.value = options.resolutionLinearScaling ?? false; + autoThresholdEnabled.value = options.autoThresholdEnabled ?? false; + autoThresholdQuantile.value = options.autoThresholdQuantile ?? 0.995; + signalDisplayMode.value = options.signalDisplayMode ?? "OBSERVED"; colormap.value = options.colormap; } @@ -69,6 +80,9 @@ export const useVisualizationOptionsStore = defineStore( resolutionScaling, resolutionLinearScaling, postLogBase, + autoThresholdEnabled, + autoThresholdQuantile, + signalDisplayMode, colormap, asVisualizationOptions, setVisualizationOptions, diff --git a/src/app/ui/MainUIComponent.vue b/src/app/ui/MainUIComponent.vue index 080f355..bc036b0 100644 --- a/src/app/ui/MainUIComponent.vue +++ b/src/app/ui/MainUIComponent.vue @@ -79,12 +79,20 @@ @openSession="onOpenSession" @agpLoaded="onAgpLoaded" @fastaLinked="onFastaLinked" + @wizardRequested="wizardOpen = true" > +
{ startOpenProgress(); try { @@ -303,7 +317,9 @@ async function openFileWithOptions( mapManager.value = newManager; networkManager.mapManager = mapManager.value; newManager.initializeMap(); - applyDefaultVisualizationPreset(); + if (options?.applyDefaultPreset !== false) { + applyDefaultVisualizationPreset(); + } if (ffname && ffname.trim() !== "") { try { const linkResponse = await networkManager.requestManager.linkFASTA( @@ -327,6 +343,14 @@ async function openFileWithOptions( } } +async function openPrimaryDatasetFromWizard( + fname: string, + ffname?: string, + options?: { applyDefaultPreset?: boolean } +): Promise { + await openFileWithOptions(fname, ffname, options); +} + function displayNewMap() { const fname = filename.value; const ffname = fastaFilename.value; @@ -389,6 +413,15 @@ function applyDefaultVisualizationPreset() { const resolutionScaling = (opt["resolutionScaling"] as boolean) ?? false; const resolutionLinearScaling = (opt["resolutionLinearScaling"] as boolean) ?? false; + const autoThresholdEnabled = + (opt["autoThresholdEnabled"] as boolean) ?? false; + const autoThresholdQuantile = + (opt["autoThresholdQuantile"] as number) ?? 0.995; + const signalDisplayMode = + opt["signalDisplayMode"] === "EXPECTED" || + opt["signalDisplayMode"] === "OBSERVED_OVER_EXPECTED" + ? (opt["signalDisplayMode"] as "EXPECTED" | "OBSERVED_OVER_EXPECTED") + : "OBSERVED"; const cmapObj = new SimpleLinearGradient( safeColorTranslator(startColor, "rgba(0,255,0,0.0)"), safeColorTranslator(endColor, "rgba(0,96,0,1.0)"), @@ -416,7 +449,10 @@ function applyDefaultVisualizationPreset() { applyCoolerWeights, resolutionScaling, resolutionLinearScaling, - finalCmap + finalCmap, + autoThresholdEnabled, + autoThresholdQuantile, + signalDisplayMode ) ); const bg = (first["backgroundColor"] as string) ?? "rgba(255,255,255,1)"; @@ -452,6 +488,9 @@ function serializeCurrentVisualizationOptions(): Record { applyCoolerWeights: options.applyCoolerWeights ?? false, resolutionScaling: options.resolutionScaling ?? false, resolutionLinearScaling: options.resolutionLinearScaling ?? false, + autoThresholdEnabled: options.autoThresholdEnabled ?? false, + autoThresholdQuantile: options.autoThresholdQuantile ?? 0.995, + signalDisplayMode: options.signalDisplayMode ?? "OBSERVED", colormap: { colormapType: cmap.colormapType, startColorRGBAString: cmap.startColorRGBA.RGBA, @@ -467,6 +506,9 @@ function serializeCurrentVisualizationOptions(): Record { applyCoolerWeights: options.applyCoolerWeights ?? false, resolutionScaling: options.resolutionScaling ?? false, resolutionLinearScaling: options.resolutionLinearScaling ?? false, + autoThresholdEnabled: options.autoThresholdEnabled ?? false, + autoThresholdQuantile: options.autoThresholdQuantile ?? 0.995, + signalDisplayMode: options.signalDisplayMode ?? "OBSERVED", colormap: { colormapType: options.colormap?.colormapType ?? "Unknown", }, @@ -585,6 +627,15 @@ async function onOpenSession(file: File): Promise { (visRaw["resolutionScaling"] as boolean) ?? false; const resolutionLinearScaling = (visRaw["resolutionLinearScaling"] as boolean) ?? false; + const autoThresholdEnabled = + (visRaw["autoThresholdEnabled"] as boolean) ?? false; + const autoThresholdQuantile = + (visRaw["autoThresholdQuantile"] as number) ?? 0.995; + const signalDisplayMode = + visRaw["signalDisplayMode"] === "EXPECTED" || + visRaw["signalDisplayMode"] === "OBSERVED_OVER_EXPECTED" + ? (visRaw["signalDisplayMode"] as "EXPECTED" | "OBSERVED_OVER_EXPECTED") + : "OBSERVED"; const cmapObj = new SimpleLinearGradient( safeColorTranslator(startColor, "rgba(0,255,0,0.0)"), safeColorTranslator(endColor, "rgba(0,96,0,1.0)"), @@ -598,7 +649,10 @@ async function onOpenSession(file: File): Promise { applyCoolerWeights, resolutionScaling, resolutionLinearScaling, - cmapObj + cmapObj, + autoThresholdEnabled, + autoThresholdQuantile, + signalDisplayMode ) ); } diff --git a/src/app/ui/components/sidebar/SavedVisualOptions.vue b/src/app/ui/components/sidebar/SavedVisualOptions.vue index bb448b1..9453cf9 100644 --- a/src/app/ui/components/sidebar/SavedVisualOptions.vue +++ b/src/app/ui/components/sidebar/SavedVisualOptions.vue @@ -402,6 +402,9 @@ function serializeVisualizationOptions(options: VisualizationOptions): Record): Visualiz applyCoolerWeights, resolutionScaling, resolutionLinearScaling, - cmap + cmap, + typeof raw.autoThresholdEnabled === "boolean" + ? raw.autoThresholdEnabled + : false, + typeof raw.autoThresholdQuantile === "number" + ? raw.autoThresholdQuantile + : 0.995, + raw.signalDisplayMode === "EXPECTED" || + raw.signalDisplayMode === "OBSERVED_OVER_EXPECTED" + ? raw.signalDisplayMode + : "OBSERVED" ); } diff --git a/src/app/ui/components/upper_ribbon/FileWizardModal.vue b/src/app/ui/components/upper_ribbon/FileWizardModal.vue new file mode 100644 index 0000000..29bc511 --- /dev/null +++ b/src/app/ui/components/upper_ribbon/FileWizardModal.vue @@ -0,0 +1,1450 @@ + + + + + + + diff --git a/src/app/ui/components/upper_ribbon/HeaderRibbon.vue b/src/app/ui/components/upper_ribbon/HeaderRibbon.vue index 19fc0a4..8461bb8 100644 --- a/src/app/ui/components/upper_ribbon/HeaderRibbon.vue +++ b/src/app/ui/components/upper_ribbon/HeaderRibbon.vue @@ -107,9 +107,15 @@
- + + +
@@ -232,6 +238,7 @@ const { applyCoolerWeights, resolutionScaling, resolutionLinearScaling, + signalDisplayMode, colormap, } = storeToRefs(visualizationOptionsStore); @@ -248,6 +255,7 @@ async function exportSvg() { applyCoolerWeights: applyCoolerWeights.value, resolutionScaling: resolutionScaling.value, resolutionLinearScaling: resolutionLinearScaling.value, + signalDisplayMode: signalDisplayMode.value, colormap: cmap instanceof SimpleLinearGradient ? { @@ -692,6 +700,15 @@ async function reloadTiles() { } } +async function onSignalDisplayModeChanged() { + try { + await props.mapManager?.visualizationManager.sendVisualizationOptionsAndReload(); + } catch (error) { + toast.error("Failed to update signal display mode"); + console.error(error); + } +} + // eslint-disable-next-line @typescript-eslint/no-unused-vars // const emit = defineEmits<{ // (e: "reloadTiles"): void; diff --git a/src/app/ui/components/upper_ribbon/NavigationBar.vue b/src/app/ui/components/upper_ribbon/NavigationBar.vue index 0c4641e..ac53404 100644 --- a/src/app/ui/components/upper_ribbon/NavigationBar.vue +++ b/src/app/ui/components/upper_ribbon/NavigationBar.vue @@ -45,6 +45,11 @@ Save --> +
  • + Wizard... +
  • CloseConvert matrices
    • +
  • + Drop caches +
    • @@ -426,6 +436,7 @@ const emit = defineEmits<{ (e: "openSession", file: File): void; (e: "agpLoaded", filename: string): void; (e: "fastaLinked", filename: string): void; + (e: "wizardRequested"): void; }>(); const props = defineProps<{ @@ -445,6 +456,10 @@ function onOpenFile() { openingFile.value = true; } +function onOpenWizard(): void { + emit("wizardRequested"); +} + function onOpenTrackManager() { trackManagerOpen.value = true; } @@ -513,6 +528,17 @@ function onConvertCoolersClicked(): void { convertingCoolers.value = true; } +async function onDropCachesClicked(): Promise { + try { + const result = await props.networkManager.requestManager.dropAllCaches(); + toast.success( + `Dropped caches: ${result.matrixMetadataDeleted} matrix metadata entries, ${result.trackCacheEntriesDeleted} track cache files` + ); + } catch (error) { + errorMessage.value = error; + } +} + function onConvertCoolersDismissed(): void { coolerToConvert.value = undefined; convertingCoolers.value = false; @@ -554,7 +580,7 @@ function onAGPFileDismissed() { openingAGPFile.value = false; } -function onFileSelected(filename: string) { +async function onFileSelected(filename: string) { if (filename && filename !== "") { const lowered = filename.toLowerCase(); if (lowered.endsWith(".hict") || lowered.endsWith(".hict.hdf5")) { @@ -565,9 +591,31 @@ function onFileSelected(filename: string) { lowered.endsWith(".cool") || lowered.endsWith(".mcool") ) { - openingFile.value = false; - coolerToConvert.value = filename; - convertingCoolers.value = true; + try { + const resolution = + await props.networkManager.requestManager.resolveMatrixSource( + filename + ); + if (resolution.action === "REUSE_CONVERTED") { + openingFile.value = false; + resolution.warnings.forEach((warning) => toast(warning)); + emit("selected", resolution.resolvedFilename); + return; + } + openingFile.value = false; + coolerToConvert.value = filename; + convertingCoolers.value = true; + resolution.warnings.forEach((warning) => + toast(warning, { + style: { + "background-color": "lightyellow", + color: "black", + }, + }) + ); + } catch (error) { + errorMessage.value = error; + } } else if (lowered.endsWith(".agp")) { openAGP(filename); } else if (lowered.endsWith(".fasta") || lowered.endsWith(".fa")) { diff --git a/src/app/ui/components/upper_ribbon/NormalizationSelector.vue b/src/app/ui/components/upper_ribbon/NormalizationSelector.vue index 80f4e16..4f49a6e 100644 --- a/src/app/ui/components/upper_ribbon/NormalizationSelector.vue +++ b/src/app/ui/components/upper_ribbon/NormalizationSelector.vue @@ -161,6 +161,44 @@
    • +
  • +
    + + +
    +
    • +
  • +
    + + + + Recomputes the colormap upper bound from the current viewport. + +
    +
    • +
  • +
    +