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feat: Added artificial row feature when no discrete feature definitio…
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…n is given
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@ShrimpCryptid
ShrimpCryptid committed Oct 31, 2024
1 parent 05e9090 commit 464d3fe
Showing 1 changed file with 57 additions and 9 deletions.
66 changes: 57 additions & 9 deletions src/state/image-dataset/csv-dataset/index.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -25,11 +25,16 @@ import {

// Some example CSV as a const here?

const exampleCsv = `${CELL_ID_KEY},${VOLUME_VIEWER_PATH},${THUMBNAIL_PATH},feature1,feature2,feature3,discretefeature
potato,https://allencell.s3.amazonaws.com/aics/nuc-morph-dataset/hipsc_fov_nuclei_timelapse_dataset/hipsc_fov_nuclei_timelapse_data_used_for_analysis/baseline_colonies_fov_timelapse_dataset/20200323_09_small/raw.ome.zarr,https://i.imgur.com/qYDFpxw.png,1,2,3,yowie
garbanzo,https://allencell.s3.amazonaws.com/aics/nuc-morph-dataset/hipsc_fov_nuclei_timelapse_dataset/hipsc_fov_nuclei_timelapse_data_used_for_analysis/baseline_colonies_fov_timelapse_dataset/20200323_09_small/raw.ome.zarr,https://i.imgur.com/JNVwCaF.jpeg,7,3.4,1,yowza
turnip,https://allencell.s3.amazonaws.com/aics/nuc-morph-dataset/hipsc_fov_nuclei_timelapse_dataset/hipsc_fov_nuclei_timelapse_data_used_for_analysis/baseline_colonies_fov_timelapse_dataset/20200323_05_large/raw.ome.zarr,https://i.pinimg.com/474x/59/79/64/59796458a1b0374d9860f4a62cf92cf1.jpg,4,5,6,yummy
rutabaga,https://allencell.s3.amazonaws.com/aics/nuc-morph-dataset/hipsc_fov_nuclei_timelapse_dataset/hipsc_fov_nuclei_timelapse_data_used_for_analysis/baseline_colonies_fov_timelapse_dataset/20200323_05_large/raw.ome.zarr,https://i.imgur.com/lA6dvOe.jpeg,9,2.8,4,yowza`;
// const exampleCsv = `${CELL_ID_KEY},${VOLUME_VIEWER_PATH},${THUMBNAIL_PATH},feature1,feature2,feature3,discretefeature
// potato,https://allencell.s3.amazonaws.com/aics/nuc-morph-dataset/hipsc_fov_nuclei_timelapse_dataset/hipsc_fov_nuclei_timelapse_data_used_for_analysis/baseline_colonies_fov_timelapse_dataset/20200323_09_small/raw.ome.zarr,https://i.imgur.com/qYDFpxw.png,1,2,3,yowie
// garbanzo,https://allencell.s3.amazonaws.com/aics/nuc-morph-dataset/hipsc_fov_nuclei_timelapse_dataset/hipsc_fov_nuclei_timelapse_data_used_for_analysis/baseline_colonies_fov_timelapse_dataset/20200323_09_small/raw.ome.zarr,https://i.imgur.com/JNVwCaF.jpeg,7,3.4,1,yowza
// turnip,https://allencell.s3.amazonaws.com/aics/nuc-morph-dataset/hipsc_fov_nuclei_timelapse_dataset/hipsc_fov_nuclei_timelapse_data_used_for_analysis/baseline_colonies_fov_timelapse_dataset/20200323_05_large/raw.ome.zarr,https://i.pinimg.com/474x/59/79/64/59796458a1b0374d9860f4a62cf92cf1.jpg,4,5,6,yummy
// rutabaga,https://allencell.s3.amazonaws.com/aics/nuc-morph-dataset/hipsc_fov_nuclei_timelapse_dataset/hipsc_fov_nuclei_timelapse_data_used_for_analysis/baseline_colonies_fov_timelapse_dataset/20200323_05_large/raw.ome.zarr,https://i.imgur.com/lA6dvOe.jpeg,9,2.8,4,yowza`;
const exampleCsv = `${CELL_ID_KEY},${VOLUME_VIEWER_PATH},${THUMBNAIL_PATH},feature1,feature2,feature3
potato,https://allencell.s3.amazonaws.com/aics/nuc-morph-dataset/hipsc_fov_nuclei_timelapse_dataset/hipsc_fov_nuclei_timelapse_data_used_for_analysis/baseline_colonies_fov_timelapse_dataset/20200323_09_small/raw.ome.zarr,https://i.imgur.com/qYDFpxw.png,1,2,3
garbanzo,https://allencell.s3.amazonaws.com/aics/nuc-morph-dataset/hipsc_fov_nuclei_timelapse_dataset/hipsc_fov_nuclei_timelapse_data_used_for_analysis/baseline_colonies_fov_timelapse_dataset/20200323_09_small/raw.ome.zarr,https://i.imgur.com/JNVwCaF.jpeg,7,3.4,1
turnip,https://allencell.s3.amazonaws.com/aics/nuc-morph-dataset/hipsc_fov_nuclei_timelapse_dataset/hipsc_fov_nuclei_timelapse_data_used_for_analysis/baseline_colonies_fov_timelapse_dataset/20200323_05_large/raw.ome.zarr,https://i.pinimg.com/474x/59/79/64/59796458a1b0374d9860f4a62cf92cf1.jpg,4,5,6
rutabaga,https://allencell.s3.amazonaws.com/aics/nuc-morph-dataset/hipsc_fov_nuclei_timelapse_dataset/hipsc_fov_nuclei_timelapse_data_used_for_analysis/baseline_colonies_fov_timelapse_dataset/20200323_05_large/raw.ome.zarr,https://i.imgur.com/lA6dvOe.jpeg,9,2.8,4`;

const reservedKeys = new Set([
CELL_ID_KEY,
Expand Down Expand Up @@ -74,15 +79,15 @@ class CsvRequest implements ImageDataset {
idToIndex: Record<string, number>;
featureInfo: Map<string, FeatureInfo>;

defaultGroupByFeatureKey: string | null;
defaultGroupByFeatureKey: string;

constructor() {
// CSV parsing library?
this.csvData = [];
this.idToIndex = {};
this.featureInfo = new Map();
this.defaultGroupByFeatureKey = "";
this.parseCsvData(exampleCsv);
this.defaultGroupByFeatureKey = null;
}

/**
Expand Down Expand Up @@ -163,6 +168,7 @@ class CsvRequest implements ImageDataset {
}

const options: Record<string, MeasuredFeaturesOption> = {};
// TODO: replace with Adobe categorical colors?
const colors = ["#e9ebee", "#c51b8a", "#fed98e", "#66c2a4", "#7f48f3", "#838383"];

for (const [value, { index, count }] of seenValues.entries()) {
Expand Down Expand Up @@ -225,6 +231,47 @@ class CsvRequest implements ImageDataset {

// Assign the first discrete feature as the default group-by feature. If none exists, construct
// an artificial discrete feature for grouping.
const firstDiscreteFeature = Array.from(this.featureInfo.values()).find(
(info) => info.type === FeatureType.DISCRETE
);
if (firstDiscreteFeature) {
this.defaultGroupByFeatureKey = firstDiscreteFeature.def.key;
}

// No discrete feature was found so we need to make one. Bin by row number, splitting into
// bins that are exponents of 10.
// So 1000 values should be 10 bins of 100, 100 values should be bins of 10, etc.
// values 1-10 should be a single bin.
const binSize = Math.max(Math.ceil(Math.log10(csvData.length)), 1) * 10;
const numBins = Math.ceil(csvData.length / binSize);
const options: Record<string, MeasuredFeaturesOption> = {};
for (let i = 0; i < numBins; i++) {
const minIndex = i * binSize;
const maxIndex = Math.min((i + 1) * binSize - 1, csvData.length - 1);
options[i.toString()] = {
// TODO: Assign color palette here
color: "#000000",
name: `Rows ${minIndex}-${maxIndex}`,
key: i.toString(),
count: maxIndex - minIndex + 1,
};
}
const rowNumberData = new Array(csvData.length).fill(0).map((_, i) => {
return Math.floor(i / binSize);
});
this.featureInfo.set("_rowNumber", {
type: FeatureType.DISCRETE,
def: {
discrete: true,
displayName: "Row Number",
description: "Row Number (auto-calculated)",
key: "_rowNumber",
tooltip: "Row Number",
options,
},
data: rowNumberData,
});
this.defaultGroupByFeatureKey = "_rowNumber";
}

private parseCsvData(csvDataSrc: string): void {
Expand Down Expand Up @@ -258,11 +305,12 @@ class CsvRequest implements ImageDataset {

// TODO: Add a discrete feature for grouping if none is available in the dataset.
const featureKeys = Array.from(this.featureInfo.keys());
console.log("Feature keys: ", featureKeys);
return Promise.resolve({
defaultXAxis: this.getFeatureKeyClamped(featureKeys, 0),
defaultYAxis: this.getFeatureKeyClamped(featureKeys, 1),
defaultColorBy: this.getFeatureKeyClamped(featureKeys, 2),
defaultGroupBy: "discretefeature",
defaultGroupBy: this.defaultGroupByFeatureKey,
// TODO: Provide the containing folder of the CSV if the values for the columns (thumbnails,
// downloads, volumes) are relative paths and not HTTPS URLs.
thumbnailRoot: "",
Expand Down Expand Up @@ -371,7 +419,7 @@ class CsvRequest implements ImageDataset {
[FOV_VOLUME_VIEWER_PATH]: data[FOV_VOLUME_VIEWER_PATH] || "",
[THUMBNAIL_PATH]: data[THUMBNAIL_PATH] || "",
[VOLUME_VIEWER_PATH]: data[VOLUME_VIEWER_PATH] || "",
[GROUP_BY_KEY]: data[GROUP_BY_KEY] || "discretefeature",
[GROUP_BY_KEY]: data[GROUP_BY_KEY] || this.defaultGroupByFeatureKey,
};
console.log(fileInfo);
return Promise.resolve(fileInfo);
Expand Down

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