hms-dbmi/viv

loadOmeTiff results in error

Dev-Lan opened this issue · 1 comments

Describe the bug
When I call the following code:

const loader = await loadOmeTiff( 
 'https://localhost:9001/PATH/FILENAME.companion.ome',
  { pool: new Pool() }
);

I get this error:
image

To Reproduce
A simplified version of my FILENAME.companion.ome file looks like this. I have removed most of the TiffData, and removed some of the irrelevant attributes. I have confirmed this still causes an error.

<?xml version="1.0" encoding="utf-8"?>
<OME xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd" xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06">
  <Image ID="Image:0" Name="FILENAME.companion.ome">
    <Pixels DimensionOrder="XYZCT" ID="Pixels:0" SizeC="1" SizeX="767" SizeY="767" SizeZ="1" Type="uint16">
      <Channel ID="Channel:0" SamplesPerPixel="1">
        <LightPath />
      </Channel>
      <TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1">
        <UUID FileName="IMAGE_FILENAME_1.tif">urn:uuid:e8e81817-232f-4c4d-a740-f8478e5ae6e8</UUID>
      </TiffData>
      <!-- More TiffData -->
    </Pixels>
  </Image>
</OME>

Additional Notes
I am able to get the companion.ome to load correctly with Fiji.

I am able to get loadMultiTiff to work correctly. E.g.

const loader = await loadMultiTiff(
    [
        [
            generateSelectionIndexRange(0, 88),
            'https://127.0.0.1:9001/PATH/IMAGE_FILENAME_1.tif',
        ],
        [
            generateSelectionIndexRange(89, 177),
            'https://127.0.0.1:9001/PATH/IMAGE_FILENAME_2.tif',
        ],
        [
            generateSelectionIndexRange(178, 215),
            'https://127.0.0.1:9001/PATH/IMAGE_FILENAME_3.tif',
        ],
    ],
    { pool: new Pool() }
);

the generateSelectionIndexRange function is a simple helper that generates a list of {c,t,z}. My data only varies in the t dimension.

Local Dev Server
I had some issues in the past that were resolved by changing my local dev server (e.g. partial requests that were longer than filesize). Currently I'm using http-server.

Environment:

  • Release or git hash: 0.13.8
  • Browser: Google Chrome
  • Browser version: 116.0.5845.187 (Official Build) (x86_64)

Can you share your data?