Less SSAO samples. Transparency fix. Constant recomputation of SASA fix. (699f0b90) · Commits · Visitlab / Chromatin / chromoskein

app/src/components/viewports/ChromatinViewport.tsx

+53 −15

Original line number	Diff line number	Diff line
		@@ -63,6 +63,8 @@ export function ChromatinViewport(props: {

		const [isShiftPressed, setShiftPressed] = useState(false);

		const [sasaGlobalValues, setSasaGlobalValues] = useState<number[][] \| null>(null);

		//~ Labeling
		let labels: GraphicsModule.Label[] = [];

		@@ -223,6 +225,45 @@ export function ChromatinViewport(props: {
		})
		}, [viewport, closestIntersection]);

		// Compute SASA values
		useEffect(() => {
		if (!viewport \|\| !configuration.data) {
		return;
		}

		const newSasa: number[][] = [];
		for (const [configurationDatumIndex, configurationDatum] of configuration.data.entries()) {
		const datum: Data \| undefined = data.data.find(d => d.id === configurationDatum.id);

		if (!datum) {
		continue;
		}

		const datumPositions = datum.values as Positions3D;
		const chromatinPart = viewport.getChromatinPartByDataId(configurationDatumIndex);

		if (!datumPositions \|\| !chromatinPart) {
		continue;
		}

		const positions = datumPositions.positions;

		if (!positions) {
		return;
		}

		const globalSasaValues = sasa(positions, {
		method: "constant",
		probe_size: configuration.sasa.probeSize,
		}, configuration.sasa.accuracy);

		newSasa.push(globalSasaValues);
		}

		setSasaGlobalValues(_ => newSasa);
		}, [viewport, data.data, configuration.data, configuration.sasa.probeSize, configuration.sasa.accuracy]);


		// Calculate/Cache Colors (1D Data Mapping + Selections)
		useEffect(() => {
		if (!viewport \|\| !configuration.data) {
		@@ -296,19 +337,19 @@ export function ChromatinViewport(props: {
		throw "Not implemented";
		}

		if (!sasaGlobalValues \|\| !sasaGlobalValues[configurationDatumIndex]) {
		continue;
		}

		//TODO: per chromosome or whole chromosome
		const globalSasaValues = sasa(positions, {
		method: configuration.sasa.method,
		probe_size: configuration.sasa.probeSize,
		}, configuration.sasa.accuracy);

		//TODO: fix underlying bug where the something sometimes don't contain last bin of the chromosome
		// if (globalSasaValues.length < chromatinPart.values.length) {
		// globalSasaValues.push(globalSasaValues.reduce((a, b) => a + b, 0) / globalSasaValues.length);
		// }
		// const globalSasaValues = sasa(positions, {
		// method: configuration.sasa.method,
		// probe_size: configuration.sasa.probeSize,
		// }, configuration.sasa.accuracy);

		const colorScale = chroma.scale(['#fcfdfd', '#010a4e']);
		newColors[configurationDatumIndex] = chromatinPart.cacheColorArray(mapScaleToChromatin(chromatinPart, globalSasaValues, colorScale));
		newColors[configurationDatumIndex] = chromatinPart.cacheColorArray(mapScaleToChromatin(chromatinPart, sasaGlobalValues[configurationDatumIndex], colorScale));
		} else if (configurationDatum.colorMappingMode == "1d-density") {
		const data1d: Array<{ chromosome: string, from: number, to: number }> \| null = data.data.find(d => d.id == isoDataID.wrap(configurationDatum.mapValues.id))?.values as Sparse1DTextData \| Sparse1DNumericData \| null;

		@@ -360,14 +401,12 @@ export function ChromatinViewport(props: {

		const numbers = [...Array(binsAmount).keys()];

		console.log(numbers);

		newColors[configurationDatumIndex] = chromatinPart.cacheColorArray(mapScaleToChromatin(chromatinPart, numbers, colorScale));
		}
		}

		setColors(() => newColors);
		}, [viewport, globalSelections.selections, configuration.data, configuration.sasa, data.data, configuration.chromosomes, configuration.density]);
		}, [viewport, globalSelections.selections, configuration.data, configuration.sasa, data.data, configuration.chromosomes, configuration.density, sasaGlobalValues]);

		// Calculate cullable bins
		useEffect(() => {
		@@ -456,7 +495,6 @@ export function ChromatinViewport(props: {
		}

		if (tool.type == ChromatinViewportToolType.PointSelection) {
		console.log('bin is: ', closestIntersection.binIndex);
		closestIntersection.chromatinPart.setBinColor(closestIntersection.binIndex, { r: selection.color.r, g: selection.color.g, b: selection.color.b, a: 1.0 });
		} else if (tool.type == ChromatinViewportToolType.SphereSelection && configuration.data[selectedDatum].selectedSelectionID) {
		// Only find position in space where the ray intersects
		@@ -710,10 +748,10 @@ export function ChromatinViewport(props: {

		const selection = globalSelections.selections.find(s => s.id == selectionId);
		if (!selection) {
		throw "No global selection found with local selection ID " + selectionId;
		throw new Error("No global selection found with local selection ID " + selectionId);
		}

		const binPositions = data.data.filter(d => d.id == datum.id)[0] as BinPositionsData;
		// const binPositions = data.data.filter(d => d.id == datum.id)[0] as BinPositionsData;

		const newBins: Uint16Array = selection.bins.slice();
		if (tool.type == ChromatinViewportToolType.PointSelection) {

app/src/modules/storage/models/selections.ts

+4 −1

Original line number	Diff line number	Diff line
		@@ -100,6 +100,9 @@ export function selectionReducer(state: SelectionState, action: SelectionAction)
		}

		const newSelections = [...state.selections];
		newSelections[selectionIndex] = {
		...state.selections[selectionIndex]
		};

		if (action.name) newSelections[selectionIndex].name = action.name;
		if (action.color) newSelections[selectionIndex].color = action.color;

libs/graphics/src/shaders/postprocess/ssao.wgsl

+5 −1

Original line number	Diff line number	Diff line
		@@ -65,8 +65,12 @@ main(@builtin(global_invocation_id) GlobalInvocationID
		let bitangent = cross(viewSpaceNormal, tangent);
		let TBN = mat3x3<f32>(tangent, bitangent, viewSpaceNormal);

		if (depth == 0.0) {
		return;
		}

		var occlusion = 0.0;
		let numberOfSamples = 32;
		let numberOfSamples = 8;
		for (var i = 0; i < numberOfSamples; i = i + 1) {
		// get sample position
		var samplePos = TBN * globals.noiseSamples[i].xyz; // from tangent to view-space

libs/graphics/src/viewports/3d_viewport.ts

+23 −23

Original line number	Diff line number	Diff line
		@@ -546,30 +546,30 @@ export class Viewport3D {
		gBufferRasterizeOpaquePass.end();

		// commandEncoder.writeTimestamp(this.timestampsQuerySet, 1);
		// const gBufferRasterizeTransparentPass = commandEncoder.beginRenderPass({
		// label: "G-Buffer Rasterization Transparent Pass",
		// colorAttachments: [
		// {
		// view: this.gBuffer.colorsTransparent.createView(),
		// clearValue: { r: 0.0, g: 0.0, b: 0.0, a: 0.0 },
		// loadOp: 'clear',
		// storeOp: 'store',
		// }
		// ]
		// });
		const gBufferRasterizeTransparentPass = commandEncoder.beginRenderPass({
		label: "G-Buffer Rasterization Transparent Pass",
		colorAttachments: [
		{
		view: this.gBuffer.colorsTransparent.createView(),
		clearValue: { r: 0.0, g: 0.0, b: 0.0, a: 0.0 },
		loadOp: 'clear',
		storeOp: 'store',
		}
		]
		});

		// gBufferRasterizeTransparentPass.setBindGroup(0, device.createBindGroup({
		// label: "Camera BG",
		// layout: bindGroupLayouts.camera,
		// entries: [
		// {
		// binding: 0, resource: { buffer: this._camera.bufferGPU, offset: 0 }
		// },
		// ]
		// }));
		// gBufferRasterizeTransparentPass.setBindGroup(2, cullObjectsBindGroup);
		// this.scene.renderRasterization(gBufferRasterizeTransparentPass, this._camera, RenderObjects.Transparent, this.depthTexture.createView());
		// gBufferRasterizeTransparentPass.end();
		gBufferRasterizeTransparentPass.setBindGroup(0, device.createBindGroup({
		label: "Camera BG",
		layout: bindGroupLayouts.camera,
		entries: [
		{
		binding: 0, resource: { buffer: this._camera.bufferGPU, offset: 0 }
		},
		]
		}));
		gBufferRasterizeTransparentPass.setBindGroup(2, cullObjectsBindGroup);
		this.scene.renderRasterization(gBufferRasterizeTransparentPass, this._camera, RenderObjects.Transparent, this.depthTexture.createView());
		gBufferRasterizeTransparentPass.end();

		//#endregion