Only check if OME-Zarr if dimension mismatch in Bioformats loader (#269)

CHANGELOG.md

@@ -6,6 +6,8 @@
 
 ### Changed
 
+- Removed greedy matching of dimension order in Bio-Formats Zarr output. Just check if OME-Zarr.
+
 ## 0.4.2
 
 ### Added

src/loaders/index.js

@@ -74,26 +74,32 @@ export async function createBioformatsZarrLoader({ url }) {
  * Specifying different dimension orders form the METADATA.ome.xml is
  * possible and necessary for creating an OME-Zarr precursor.
  *
- * e.g. `bioformats2raw --file_type=zarr --dimension-order='XYZCY'`
+ * e.g. `bioformats2raw --file_type=zarr --dimension-order='XYZCT'`
  *
- * Here we check the shape of base of the pyrmaid and compare the shape
- * to the shape of the dimensions. If they are different, we reorder the
- * dimensions to create the zarr loader. This is fragile code, and will only
- * be executed if someone tries to specify different dimension orders.
+ * This is fragile code, and will only be executed if someone
+ * tries to specify different dimension orders.
  */
  const nonXYShape = shape.slice(0, -2); // XY always last dims and don't need to be compared
  const nonXYDims = dimensions.filter(d => d.values); // XY are null
  const allSameSize = nonXYShape.every(
  (s, i) => s === nonXYDims[i].values.length
  );
  if (!allSameSize) {
- const sortedDims = [];
- // Greedily match first matching dimension
- nonXYShape.forEach(len => {
- const firstMatchedDim = nonXYDims.filter(d => d.values.length === len)[0];
- sortedDims.push(firstMatchedDim);
- });
- const newDimensions = [...sortedDims, ...dimensions.slice(-2)]; // append YX dims
+ // Assume OME-Zarr, dims === XYZCT
+ const omeZarrDims = [
+ nonXYDims.filter(d => d.field === 'time')[0],
+ nonXYDims.filter(d => d.field === 'channel')[0],
+ nonXYDims.filter(d => d.field === 'z')[0]
+ ];
+ // compare sizes of sorted dims
+ if (
+ !omeZarrDims.every(({ values }, i) => values.length === nonXYShape[i])
+ ) {
+ throw Error(
+ `Dimension order is different from METADATA.ome.xml and isn't OME-Zarr.`
+ );
+ }
+ const newDimensions = [...omeZarrDims, ...dimensions.slice(-2)]; // append YX dims
  return new ZarrLoader({ data, dimensions: newDimensions });
  }