From fa75154737d5de62f66587b50b33910412d2745a Mon Sep 17 00:00:00 2001
From: Jeff Peck <jeffrey.peck@10xgenomics.com>
Date: Fri, 12 May 2023 18:18:29 -0400
Subject: [PATCH] be more forgiving when fileDirectory.SampleFormat does not
 have all values populated, such as in bioformats ome tif files

---
 src/geotiffimage.js | 45 ++++++++++++++++++++++++---------------------
 1 file changed, 24 insertions(+), 21 deletions(-)

diff --git a/src/geotiffimage.js b/src/geotiffimage.js
index 21994643..12281d42 100644
--- a/src/geotiffimage.js
+++ b/src/geotiffimage.js
@@ -1,12 +1,12 @@
 /** @module geotiffimage */
-import { getFloat16 } from '@petamoriken/float16';
+import {getFloat16} from '@petamoriken/float16';
 import getAttribute from 'xml-utils/get-attribute.js';
 import findTagsByName from 'xml-utils/find-tags-by-name.js';
 
-import { photometricInterpretations, ExtraSamplesValues } from './globals.js';
-import { fromWhiteIsZero, fromBlackIsZero, fromPalette, fromCMYK, fromYCbCr, fromCIELab } from './rgb.js';
-import { getDecoder } from './compression/index.js';
-import { resample, resampleInterleaved } from './resample.js';
+import {photometricInterpretations, ExtraSamplesValues} from './globals.js';
+import {fromWhiteIsZero, fromBlackIsZero, fromPalette, fromCMYK, fromYCbCr, fromCIELab} from './rgb.js';
+import {getDecoder} from './compression/index.js';
+import {resample, resampleInterleaved} from './resample.js';
 
 /**
  * @typedef {Object} ReadRasterOptions
@@ -295,8 +295,8 @@ class GeoTIFFImage {
   }
 
   getReaderForSample(sampleIndex) {
-    const format = this.fileDirectory.SampleFormat
-      ? this.fileDirectory.SampleFormat[sampleIndex] : 1;
+    const format = this.getSampleFormat(sampleIndex);
+
     const bitsPerSample = this.fileDirectory.BitsPerSample[sampleIndex];
     switch (format) {
       case 1: // unsigned integer data
@@ -339,7 +339,8 @@ class GeoTIFFImage {
 
   getSampleFormat(sampleIndex = 0) {
     return this.fileDirectory.SampleFormat
-      ? this.fileDirectory.SampleFormat[sampleIndex] : 1;
+      ? (this.fileDirectory.SampleFormat[sampleIndex] ?? Math.max.apply(null, this.fileDirectory.SampleFormat))
+      : 1;
   }
 
   getBitsPerSample(sampleIndex = 0) {
@@ -366,7 +367,7 @@ class GeoTIFFImage {
     const numTilesPerRow = Math.ceil(this.getWidth() / this.getTileWidth());
     const numTilesPerCol = Math.ceil(this.getHeight() / this.getTileHeight());
     let index;
-    const { tiles } = this;
+    const {tiles} = this;
     if (this.planarConfiguration === 1) {
       index = (y * numTilesPerRow) + x;
     } else if (this.planarConfiguration === 2) {
@@ -382,11 +383,11 @@ class GeoTIFFImage {
       offset = this.fileDirectory.StripOffsets[index];
       byteCount = this.fileDirectory.StripByteCounts[index];
     }
-    const slice = (await this.source.fetch([{ offset, length: byteCount }], signal))[0];
+    const slice = (await this.source.fetch([{offset, length: byteCount}], signal))[0];
 
     let request;
     if (tiles === null || !tiles[index]) {
-    // resolve each request by potentially applying array normalization
+      // resolve each request by potentially applying array normalization
       request = (async () => {
         let data = await poolOrDecoder.decode(this.fileDirectory, slice);
         const sampleFormat = this.getSampleFormat();
@@ -415,7 +416,7 @@ class GeoTIFFImage {
     }
 
     // cache the tile request
-    return { x, y, sample, data: await request };
+    return {x, y, sample, data: await request};
   }
 
   /**
@@ -434,7 +435,7 @@ class GeoTIFFImage {
    * @returns {Promise<ReadRasterResult>}
    */
   async _readRaster(imageWindow, samples, valueArrays, interleave, poolOrDecoder, width,
-    height, resampleMethod, signal) {
+                    height, resampleMethod, signal) {
     const tileWidth = this.getTileWidth();
     const tileHeight = this.getTileHeight();
     const imageWidth = this.getWidth();
@@ -466,7 +467,7 @@ class GeoTIFFImage {
     }
 
     const promises = [];
-    const { littleEndian } = this;
+    const {littleEndian} = this;
 
     for (let yTile = minYTile; yTile < maxYTile; ++yTile) {
       for (let xTile = minXTile; xTile < maxXTile; ++xTile) {
@@ -517,7 +518,7 @@ class GeoTIFFImage {
     await Promise.all(promises);
 
     if ((width && (imageWindow[2] - imageWindow[0]) !== width)
-        || (height && (imageWindow[3] - imageWindow[1]) !== height)) {
+      || (height && (imageWindow[3] - imageWindow[1]) !== height)) {
       let resampled;
       if (interleave) {
         resampled = resampleInterleaved(
@@ -558,9 +559,9 @@ class GeoTIFFImage {
    * @returns {Promise<ReadRasterResult>} the decoded arrays as a promise
    */
   async readRasters({
-    window: wnd, samples = [], interleave, pool = null,
-    width, height, resampleMethod, fillValue, signal,
-  } = {}) {
+                      window: wnd, samples = [], interleave, pool = null,
+                      width, height, resampleMethod, fillValue, signal,
+                    } = {}) {
     const imageWindow = wnd || [0, 0, this.getWidth(), this.getHeight()];
 
     // check parameters
@@ -638,8 +639,10 @@ class GeoTIFFImage {
    *                                       to be aborted
    * @returns {Promise<ReadRasterResult>} the RGB array as a Promise
    */
-  async readRGB({ window, interleave = true, pool = null, width, height,
-    resampleMethod, enableAlpha = false, signal } = {}) {
+  async readRGB({
+                  window, interleave = true, pool = null, width, height,
+                  resampleMethod, enableAlpha = false, signal
+                } = {}) {
     const imageWindow = window || [0, 0, this.getWidth(), this.getHeight()];
 
     // check parameters
@@ -697,7 +700,7 @@ class GeoTIFFImage {
       resampleMethod,
       signal,
     };
-    const { fileDirectory } = this;
+    const {fileDirectory} = this;
     const raster = await this.readRasters(subOptions);
 
     const max = 2 ** this.fileDirectory.BitsPerSample[0];