@aics/vole-core 3.14.1 → 3.15.0

package/es/FusedChannelData.js

@@ -7,7 +7,7 @@ const fuseShaderSrcF = "precision highp float;\nprecision highp int;\nprecision
 /* babel-plugin-inline-import './constants/shaders/fuseI.frag' */
 const fuseShaderSrcI = "precision highp float;\nprecision highp int;\nprecision highp sampler2D;\nprecision highp sampler3D;\n\n// the lut texture is a 256x1 rgba texture for each channel\nuniform sampler2D lutSampler;\n\nuniform vec2 lutMinMax;\n\n// src texture is the raw volume intensity data\nuniform isampler2D srcTexture;\n\nvoid main()\n{\n    ivec2 vUv = ivec2(int(gl_FragCoord.x), int(gl_FragCoord.y));\n    int intensity = texelFetch(srcTexture, vUv, 0).r;\n    float ilookup = float(float(intensity) - lutMinMax.x) / float(lutMinMax.y - lutMinMax.x);\n    // apply lut to intensity:\n    vec4 pix = texture(lutSampler, vec2(ilookup, 0.5));\n    gl_FragColor = vec4(pix.xyz*pix.w, pix.w);\n}\n";
 /* babel-plugin-inline-import './constants/shaders/colorizeUI.frag' */
-const colorizeSrcUI = "precision highp float;\nprecision highp int;\nprecision highp usampler2D;\nprecision highp sampler3D;\n\nuniform sampler2D featureData;\n/** Min and max feature values that define the endpoints of the color map. Values\n * outside the range will be clamped to the nearest endpoint.\n */\nuniform float featureColorRampMin;\nuniform float featureColorRampMax;\nuniform sampler2D colorRamp;\nuniform usampler2D inRangeIds;\nuniform usampler2D outlierData;\n\n/** \n * Offsets raw IDs sampled from the volume data to get the global\n * ID used to index into the feature and outlier data.\n*/\nuniform uint idOffset;\n\nuniform vec3 outlineColor;\n\n/** MUST be synchronized with the DrawMode enum in ColorizeCanvas! */\nconst uint DRAW_MODE_HIDE = 0u;\nconst uint DRAW_MODE_COLOR = 1u;\n\nuniform vec3 outlierColor;\nuniform uint outlierDrawMode;\nuniform vec3 outOfRangeColor;\nuniform uint outOfRangeDrawMode;\n\nuniform uint highlightedId;\n\nuniform bool hideOutOfRange;\n\n// src texture is the raw volume intensity data\nuniform usampler2D srcTexture;\n\nuint getId(ivec2 uv) {\n  uint rawId = texelFetch(srcTexture, uv, 0).r;\n  if (rawId == 0u) {\n    return 0u;\n  }\n  return rawId + idOffset;\n}\nvec4 getFloatFromTex(sampler2D tex, int index) {\n  int width = textureSize(tex, 0).x;\n  ivec2 featurePos = ivec2(index % width, index / width);\n  return texelFetch(tex, featurePos, 0);\n}\nuvec4 getUintFromTex(usampler2D tex, int index) {\n  int width = textureSize(tex, 0).x;\n  ivec2 featurePos = ivec2(index % width, index / width);\n  return texelFetch(tex, featurePos, 0);\n}\nvec4 getColorRamp(float val) {\n  float width = float(textureSize(colorRamp, 0).x);\n  float range = (width - 1.0) / width;\n  float adjustedVal = (0.5 / width) + (val * range);\n  return texture(colorRamp, vec2(adjustedVal, 0.5));\n}\nvec4 getColorFromDrawMode(uint drawMode, vec3 defaultColor) {\n  const uint DRAW_MODE_HIDE = 0u;\n  vec3 backgroundColor = vec3(0.0, 0.0, 0.0);\n  if (drawMode == DRAW_MODE_HIDE) {\n    return vec4(backgroundColor, 0.0);\n  } else {\n    return vec4(defaultColor, 1.0);\n  }\n}\n\nfloat getFeatureVal(uint id) {\n  // Data buffer starts at 0, non-background segmentation IDs start at 1\n  return getFloatFromTex(featureData, int(id) - 1).r;\n}\nuint getOutlierVal(uint id) {\n  // Data buffer starts at 0, non-background segmentation IDs start at 1\n  return getUintFromTex(outlierData, int(id) - 1).r;\n}\nbool getIsInRange(uint id) {\n  return getUintFromTex(inRangeIds, int(id) - 1).r == 1u;\n}\nbool getIsOutlier(float featureVal, uint outlierVal) {\n  return isinf(featureVal) || outlierVal != 0u;\n}\n\nvec4 getObjectColor(ivec2 sUv, float opacity) {\n  // Get the segmentation id at this pixel\n  uint id = getId(sUv);\n\n  // A segmentation id of 0 represents background\n  if (id == 0u) {\n    return vec4(0, 0, 0, 0);\n  }\n\n  // color the highlighted object\n  if (id == highlightedId) {\n    return vec4(outlineColor, 1.0);\n  }\n\n  float featureVal = getFeatureVal(id);\n  uint outlierVal = getOutlierVal(id);\n  float normFeatureVal = (featureVal - featureColorRampMin) / (featureColorRampMax - featureColorRampMin);\n\n  // Use the selected draw mode to handle out of range and outlier values;\n  // otherwise color with the color ramp as usual.\n  bool isInRange = getIsInRange(id);\n  bool isOutlier = getIsOutlier(featureVal, outlierVal);\n\n  // Features outside the filtered/thresholded range will all be treated the same (use `outOfRangeDrawColor`).\n  // Features inside the range can either be outliers or standard values, and are colored accordingly.\n  vec4 color;\n  if (isInRange) {\n    if (isOutlier) {\n      color = getColorFromDrawMode(outlierDrawMode, outlierColor);\n    } else {\n      color = getColorRamp(normFeatureVal);\n    }\n  } else {\n    color = getColorFromDrawMode(outOfRangeDrawMode, outOfRangeColor);\n  }\n  color.a *= opacity;\n  return color;\n}\n\nvoid main() {\n  ivec2 vUv = ivec2(int(gl_FragCoord.x), int(gl_FragCoord.y));\n  gl_FragColor = getObjectColor(vUv, 1.0);\n}\n";
+const colorizeSrcUI = "precision highp float;\nprecision highp int;\nprecision highp usampler2D;\nprecision highp sampler3D;\n\nuniform sampler2D featureData;\n/** Min and max feature values that define the endpoints of the color map. Values\n * outside the range will be clamped to the nearest endpoint.\n */\nuniform float featureColorRampMin;\nuniform float featureColorRampMax;\nuniform sampler2D colorRamp;\nuniform usampler2D inRangeIds;\nuniform usampler2D outlierData;\n\n/**\n * LUT mapping from the segmentation ID (raw pixel value) to the\n * global ID (index in data buffers like `featureData` and `outlierData`).\n * \n * For a given segmentation ID `segId`, the global ID is given by:\n * `segIdToGlobalId[segId - segIdOffset] - 1`.\n*/\nuniform usampler2D segIdToGlobalId;\nuniform uint segIdOffset;\n\nuniform vec3 outlineColor;\n\n/** MUST be synchronized with the DrawMode enum in ColorizeCanvas! */\nconst uint DRAW_MODE_HIDE = 0u;\nconst uint DRAW_MODE_COLOR = 1u;\nconst uint BACKGROUND_ID = 0u;\nconst uint MISSING_DATA_ID = 0xFFFFFFFFu;\n\nuniform vec3 outlierColor;\nuniform uint outlierDrawMode;\nuniform vec3 outOfRangeColor;\nuniform uint outOfRangeDrawMode;\n\nuniform uint highlightedId;\n\nuniform bool hideOutOfRange;\n\n// src texture is the raw volume intensity data\nuniform usampler2D srcTexture;\n\nvec4 getFloatFromTex(sampler2D tex, int index) {\n  int width = textureSize(tex, 0).x;\n  ivec2 featurePos = ivec2(index % width, index / width);\n  return texelFetch(tex, featurePos, 0);\n}\nuvec4 getUintFromTex(usampler2D tex, int index) {\n  int width = textureSize(tex, 0).x;\n  ivec2 featurePos = ivec2(index % width, index / width);\n  return texelFetch(tex, featurePos, 0);\n}\nuint getId(ivec2 uv) {\n  uint rawId = texelFetch(srcTexture, uv, 0).r;\n  if (rawId == 0u) {\n    return BACKGROUND_ID;\n  }\n  uvec4 c = getUintFromTex(segIdToGlobalId, int(rawId - segIdOffset));\n  // Note: IDs are offset by `1` to reserve `0` for segmentations that don't\n  // have associated data. `1` MUST be subtracted from the ID when accessing\n  // data buffers.\n  uint globalId = c.r;\n  if (globalId == 0u) {\n    return MISSING_DATA_ID;\n  }\n  return globalId;\n}\nvec4 getColorRamp(float val) {\n  float width = float(textureSize(colorRamp, 0).x);\n  float range = (width - 1.0) / width;\n  float adjustedVal = (0.5 / width) + (val * range);\n  return texture(colorRamp, vec2(adjustedVal, 0.5));\n}\nvec4 getColorFromDrawMode(uint drawMode, vec3 defaultColor) {\n  const uint DRAW_MODE_HIDE = 0u;\n  vec3 backgroundColor = vec3(0.0, 0.0, 0.0);\n  if (drawMode == DRAW_MODE_HIDE) {\n    return vec4(backgroundColor, 0.0);\n  } else {\n    return vec4(defaultColor, 1.0);\n  }\n}\n\nfloat getFeatureVal(uint id) {\n  // Data buffer starts at 0, non-background segmentation IDs start at 1\n  return getFloatFromTex(featureData, int(id) - 1).r;\n}\nuint getOutlierVal(uint id) {\n  // Data buffer starts at 0, non-background segmentation IDs start at 1\n  return getUintFromTex(outlierData, int(id) - 1).r;\n}\nbool getIsInRange(uint id) {\n  return getUintFromTex(inRangeIds, int(id) - 1).r == 1u;\n}\nbool getIsOutlier(float featureVal, uint outlierVal) {\n  return isinf(featureVal) || outlierVal != 0u;\n}\n\nvec4 getObjectColor(ivec2 sUv, float opacity) {\n  // Get the segmentation id at this pixel\n  uint id = getId(sUv);\n\n  // A segmentation id of 0 represents background\n  if (id == BACKGROUND_ID) {\n    return vec4(0, 0, 0, 0);\n  }\n\n  // color the highlighted object. Note, `highlightedId` is a 0-based index\n  // (global ID w/o offset), while `id` is a 1-based index.\n  if (id - 1u == highlightedId) {\n    return vec4(outlineColor, 1.0);\n  }\n\n  float featureVal = getFeatureVal(id);\n  uint outlierVal = getOutlierVal(id);\n  float normFeatureVal = (featureVal - featureColorRampMin) / (featureColorRampMax - featureColorRampMin);\n\n  // Use the selected draw mode to handle out of range and outlier values;\n  // otherwise color with the color ramp as usual.\n  bool isInRange = getIsInRange(id);\n  bool isOutlier = getIsOutlier(featureVal, outlierVal);\n  bool isMissingData = (id == MISSING_DATA_ID);\n\n  // Features outside the filtered/thresholded range will all be treated the same (use `outOfRangeDrawColor`).\n  // Features inside the range can either be outliers or standard values, and are colored accordingly.\n  vec4 color;\n  if (isMissingData) { \n    // TODO: Add color controls for missing data\n    color = getColorFromDrawMode(outlierDrawMode, outlierColor);\n  } else if (isInRange) {\n    if (isOutlier) {\n      color = getColorFromDrawMode(outlierDrawMode, outlierColor);\n    } else {\n      color = getColorRamp(normFeatureVal);\n    }\n  } else {\n    color = getColorFromDrawMode(outOfRangeDrawMode, outOfRangeColor);\n  }\n  color.a *= opacity;\n  return color;\n}\n\nvoid main() {\n  ivec2 vUv = ivec2(int(gl_FragCoord.x), int(gl_FragCoord.y));\n  gl_FragColor = getObjectColor(vUv, 1.0);\n}\n";
 // This is the owner of the fused RGBA volume texture atlas, and the mask texture atlas.
 // This module is responsible for updating the fused texture, given the read-only volume channel data.
 export default class FusedChannelData {
@@ -125,7 +125,10 @@ export default class FusedChannelData {
         hideOutOfRange: {
           value: false
         },
-        idOffset: {
+        segIdToGlobalId: {
+          value: new DataTexture()
+        },
+        segIdOffset: {
           value: 0
         }
       },
@@ -222,10 +225,17 @@ export default class FusedChannelData {
           mat.uniforms.outlierDrawMode.value = feature.outlierDrawMode;
           mat.uniforms.outOfRangeDrawMode.value = feature.outOfRangeDrawMode;
           mat.uniforms.hideOutOfRange.value = feature.hideOutOfRange;
-          // Offset IDs based on the current frame, for data without
-          // globally-unique IDs.
-          const idOffset = feature.timeToIdOffset[channels[chIndex].time] ?? 0;
-          mat.uniforms.idOffset.value = idOffset;
+          const time = channels[chIndex].time;
+          let globalIdLookupInfo = feature.frameToGlobalIdLookup.get(time);
+          if (!globalIdLookupInfo) {
+            console.warn(`FusedChannelData.gpuFuse: No global ID lookup info for time ${time} in channel ${chIndex}. A default lookup will be used, which may cause visual artifacts.`);
+            globalIdLookupInfo = {
+              texture: new DataTexture(Uint32Array[0]),
+              minSegId: 1
+            };
+          }
+          mat.uniforms.segIdToGlobalId.value = globalIdLookupInfo.texture;
+          mat.uniforms.segIdOffset.value = globalIdLookupInfo.minSegId;
         } else {
           // the lut texture is spanning only the data range of the channel, not the datatype range
           mat.uniforms.lutMinMax.value = new Vector2(channels[chIndex].rawMin, channels[chIndex].rawMax);

package/es/types/types.d.ts

@@ -31,17 +31,28 @@ export interface ColorizeFeature {
     idsToFeatureValue: DataTexture;
     featureValueToColor: DataTexture;
     /**
-     * A mapping from the current frame number to the ID offset for that frame.
-     * This is used for data where the raw IDs are not globally-unique. Adding the
-     * offset to the raw ID gives the unique, global ID that can be used to index
-     * into the `idsToFeatureValue` and other colorize-related data textures.
+     * Maps from a frame number to an info object used to look up the global ID
+     * from a given segmentation ID (raw pixel value) on that frame. The info
+     * object contains a texture and a minimum segmentation ID for that frame, the
+     * latter of which is used to minimize the memory footprint of the lookup
+     * table.
      *
-     * For each raw ID `i` at some time `t`, the global ID is `i +
-     * timeToIdOffset[t]`.
+     * For a frame at time `t`, the global ID of a segmentation `segId` is given
+     * by:
+     * ```
+     * lookup[t].texture.getAt(segId - lookup[t].minSegId) - 1
+     * ```
+     * The result is `-1` if there is no global ID for that segmentation ID on
+     * that frame.
      *
-     * If raw IDs are globally-unique, this array should be all zeros.
+     * The global ID can be used directly as an index into the
+     * `idsToFeatureValue`, `inRangeIds`, and `outlierData` data textures to get
+     * values for that segmentation ID.
      */
-    timeToIdOffset: Uint32Array;
+    frameToGlobalIdLookup: Map<number, {
+        texture: DataTexture;
+        minSegId: number;
+    }>;
     inRangeIds: DataTexture;
     outlierData: DataTexture;
     featureMin: number;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@aics/vole-core",
-  "version": "3.14.1",
+  "version": "3.15.0",
   "description": "volume renderer for 3d, 4d, or 5d imaging data with OME-Zarr support",
   "main": "es/index.js",
   "type": "module",