Extend image metadata

[kostrykin]

This PR adds a series of basic metadata elements for image data, including:

• The width, height, depth of the image, as well as the number of channels and frames (the terminology is consistent with Add support for arbitrarily ordered image axes in image content assertions #18891)
• The axes of the image (e.g., YXC or ZCYX)
• dtype: The data type of the image pixels or voxels (e.g., uint8 or float64)
• num_unique_values: The number of unique values in the image

This is useful to define validators for input data when working with images. Some examples of when this will be useful:

• Require that an image is a binary image by validating that num_unique_values is 1 or 2.
• Validate dtype: Some tools might not support float but only int image data (or vice versa).
• Validate that channels is 0 or 1: Restrict input data to single-channel images.
• Validate axes, depth, channels, frames: Require that an image has one or more z-slices / channels / time steps.

TIFF files are read using the tifffile library, other image types are tried to be read using Pillow. The new metadata is defined as optional, because Pillow might not be installed, or it might not be possible to read an image using Pillow (e.g., due to an image format that Pillow does not support).

For multi-page TIFF files, the metadata is determined for each page individually, and then joined into a ,-separated string provided as a JSON-encoded list of items (with the order corresponding to the order of the pages in the series).

How to test the changes?

(Select all options that apply)

• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
• Instructions for manual testing are as follows:
  1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

• I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

[bernt-matthias]

The problem with black will be solved here #18955

[bernt-matthias]

Just had the same problem and my solution for this was 887b1aa

[kostrykin]

Thanks @bernt-matthias this solved it.

[mvdbeek]

The integration test failures look real, is that because of a missing library ?

FAILED test/integration/test_datatype_upload.py::test_upload_datatype_auto[im_empty.tif] - AssertionError: assert 'binary' == 'tiff'
  - tiff
  + binary
FAILED test/integration/test_datatype_upload.py::test_upload_datatype_auto[im4_float.tif] - AssertionError: assert 'binary' == 'tiff'
  - tiff
  + binary
= 2 failed, 246 passed, 18 skipped, 2 xpassed, 1063 warnings in 4159.23s (1:09:19) =

[mvdbeek]

Also know that the files placed in lib/galaxy/datatypes/test must match the datatype, so if you're placing invalid files there you have to change the extension.

[kostrykin]

I think I found the issue. Image files currently use Pillow for sniffing the image type:

• galaxy/lib/galaxy/datatypes/images.py

  Line 67 in 43984c1

  return check_image_type(filename, self.image_formats)

• galaxy/lib/galaxy/util/image_util.py

  Line 32 in 43984c1

  fmt = image_type(filename)

However, reading these two images with Pillow fails.

---

Edit: This is now fixed in 8432024. TIFFs are now sniffed using tifffile, which is more reliable than Pillow. In addition, im_corrupted.tif is removed in 9a8d944, because it isn't recognized as a TIFF file by tifffile anyways.

[github-actions]

This PR was merged without a "kind/" label, please correct.

[mvdbeek]

Thanks a lot @kostrykin!