Add support for reading compressed NDPI tiles #4181

melissalinkert · 2024-04-12T16:21:09Z

This expands on the "precompressed" features added in #3992.

The main goal was to just add compressed tile reading to the NDPI reader, so that conversion from NDPI to DICOM wouldn't require much if any recompression. This required a variety of changes not limited to NDPI though:

update JPEGTurboService so that the repackaged compressed tiles can be retrieved, as well as the tile size and counts
move general TIFF tile copying logic out of SVSReader, and into MinimalTiffReader (to prevent duplicate logic in NDPIReader)
- this should also make it easier to support precompressed tiles in other TIFF-based formats later on
update NDPIReader to report optimal sizes based on actual IFD/JPEG stream, instead of constant 1024x1024
update DicomWriter to allow different tile sizes in each resolution, since NDPI reports different sizes per resolution
update NDPIReader to use the saveCompressedBytes API

The end result is that something like this should now work:

bfconvert -noflat -precompressed -compression JPEG CMU-1.ndpi cmu.dcm

and should complete within a few seconds as all tiles can be copied without any recompression.

I would not expect SVS -> DICOM support to change, but it probably makes sense to double-check just in case the refactoring caused any problems.

I don't expect this to fail tests, but excluding for now so this doesn't distract from 7.3.0. Given the API changes in JPEGTurboService, this probably does require a major version.

cc @dclunie, @fedorov

This provides better precompressed tile support for input formats that don't have a constant tile size across all resolutions.

sbesson

Generally, very supportive of the migration of the SVS functionality for accessing the raw tiles to MinimalTiffReader. Beyond the scope of this change, it opens the door to supporting the reading of compressed tiles in other TIFF-based whole slide image formats. Also this starts exposing an initial API allowing direct raw tile access in TIFF formats from Bio-Formats.

Using the reference CMU-1.svs and CMU-1.npdi from https://openslide.cs.cmu.edu/download/openslide-testdata/, I was able to successfully run bfconvert -noflat -precompressed -compression JPEG into a DICOM file which has a sensible size.

However, the changes seem to have affected conversion with other options (no -precompressed flag or JPEG-2000 compression) as the utility now fails with an java.lang.ArrayIndexOutOfBoundsException

+ mkdir from_svs_precompressed_jpeg
+ /Users/sbesson/Documents/GitHub/bioformats/tools/bfconvert -noflat -precompressed -compression JPEG CMU-1.svs from_svs_precompressed_jpeg/CMU-1.dcm
+ mkdir from_svs_precompressed_j2k
+ /Users/sbesson/Documents/GitHub/bioformats/tools/bfconvert -noflat -precompressed -compression JPEG-2000 CMU-1.svs from_svs_precompressed_j2k/CMU-1.dcm
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1
	at loci.formats.out.DicomWriter.saveBytes(DicomWriter.java:587)
	at loci.formats.ImageWriter.saveBytes(ImageWriter.java:260)
	at loci.formats.tools.ImageConverter.convertTilePlane(ImageConverter.java:1076)
	at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:908)
	at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:841)
	at loci.formats.tools.ImageConverter.main(ImageConverter.java:1318)
+ mkdir from_svs_jpeg
+ /Users/sbesson/Documents/GitHub/bioformats/tools/bfconvert -noflat -compression JPEG CMU-1.svs from_svs_jpeg/CMU-1.dcm
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1
	at loci.formats.out.DicomWriter.saveBytes(DicomWriter.java:587)
	at loci.formats.ImageWriter.saveBytes(ImageWriter.java:260)
	at loci.formats.tools.ImageConverter.convertTilePlane(ImageConverter.java:1076)
	at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:908)
	at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:841)
	at loci.formats.tools.ImageConverter.main(ImageConverter.java:1318)
+ mkdir from_svs_j2k
+ /Users/sbesson/Documents/GitHub/bioformats/tools/bfconvert -noflat -compression JPEG-2000 CMU-1.svs from_svs_j2k/CMU-1.dcm
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1
	at loci.formats.out.DicomWriter.saveBytes(DicomWriter.java:587)
	at loci.formats.ImageWriter.saveBytes(ImageWriter.java:260)
	at loci.formats.tools.ImageConverter.convertTilePlane(ImageConverter.java:1076)
	at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:908)
	at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:841)
	at loci.formats.tools.ImageConverter.main(ImageConverter.java:1318)
+ mkdir from_ndpi_precompressed_jpeg
+ /Users/sbesson/Documents/GitHub/bioformats/tools/bfconvert -noflat -precompressed -compression JPEG CMU-1.ndpi from_ndpi_precompressed_jpeg/CMU-1.dcm
+ mkdir from_ndpi_precompressed_j2k
+ /Users/sbesson/Documents/GitHub/bioformats/tools/bfconvert -noflat -precompressed -compression JPEG-2000 CMU-1.ndpi from_ndpi_precompressed_j2k/CMU-1.dcm
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1
	at loci.formats.out.DicomWriter.saveBytes(DicomWriter.java:587)
	at loci.formats.ImageWriter.saveBytes(ImageWriter.java:260)
	at loci.formats.tools.ImageConverter.convertTilePlane(ImageConverter.java:1076)
	at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:908)
	at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:841)
	at loci.formats.tools.ImageConverter.main(ImageConverter.java:1318)
+ mkdir from_ndpi_jpeg
+ /Users/sbesson/Documents/GitHub/bioformats/tools/bfconvert -noflat -compression JPEG CMU-1.ndpi from_ndpi_jpeg/CMU-1.dcm
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1
	at loci.formats.out.DicomWriter.saveBytes(DicomWriter.java:587)
	at loci.formats.ImageWriter.saveBytes(ImageWriter.java:260)
	at loci.formats.tools.ImageConverter.convertTilePlane(ImageConverter.java:1076)
	at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:908)
	at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:841)
	at loci.formats.tools.ImageConverter.main(ImageConverter.java:1318)
+ mkdir from_ndpi_j2k
+ /Users/sbesson/Documents/GitHub/bioformats/tools/bfconvert -noflat -compression JPEG-2000 CMU-1.ndpi from_ndpi_j2k/CMU-1.dcm
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1
	at loci.formats.out.DicomWriter.saveBytes(DicomWriter.java:587)
	at loci.formats.ImageWriter.saveBytes(ImageWriter.java:260)
	at loci.formats.tools.ImageConverter.convertTilePlane(ImageConverter.java:1076)
	at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:908)
	at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:841)
	at loci.formats.tools.ImageConverter.main(ImageConverter.java:1318)

I retested with Bio-Formats 7.3.0 and confirm that bfconvert -noflat -compression JPEG CMU-1.svs from_svs_jpeg/CMU-1.dcm was running to completion so I suspect this is a regression introduced by this PR.

melissalinkert · 2024-06-20T23:37:19Z

I believe the exceptions in #4181 (review) are all fixed by 23780de.

sbesson

With the latest fixes, the conversion utility completed in all my tests. Tables below give the execution times measured in seconds with a standard deviation computed from 3 runs.

Using Bio-Formats 7.3.0 and CMU-1.svs

Compression / Precompressed	yes	No
JPEG	78.6 +/- 0.6	228.4 +/- 2.2
JPEG-2000	682.8 +/- 5.6	674.0 +/- 11.0

Using this PR and CMU-1.svs

Compression / Precompressed	yes	No
JPEG	80.6 +/- 1.1	231.9 +/- 2.3
JPEG-2000	686.4 +/- 4.2	684.8 +/- 3.6

Using this PR and CMU-1.ndpi

Compression / Precompressed	yes	No
JPEG	15.7 +/- 0.4	116.9 +/- 7.2
JPEG-2000	648.7 +/- 4.5	645.9 +/- 2.6

Measurements are consistent with the previous values and as per above, there is a substantial gain of performance (even better than SVS) when using the precompressed flag and the native tile compression (JPEG).

Loading the generated DICOM files into OMERO for visual assessment and comparison to the original, all datasets worked as expected with the exception of the DICOM dataset created from the SVS file using -precompressed and -compression JPEG-2000 as the import failed with

java.lang.RuntimeException: Failure response on import!
Category: ::omero::grid::ImportRequest
Name: import-request-failure
Parameters: {stacktrace=java.lang.RuntimeException: File is neither valid JP2 file nor valid JPEG 2000 codestream
	at com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState.initializeRead(J2KReadState.java:729)
	at com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState.<init>(J2KReadState.java:241)
	at com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader.readRaster(J2KImageReader.java:551)
	at ome.codecs.services.JAIIIOServiceImpl.readRaster(JAIIIOServiceImpl.java:177)
	at ome.codecs.JPEG2000Codec.decompress(JPEG2000Codec.java:296)
	at loci.formats.codec.WrappedCodec.decompress(WrappedCodec.java:86)
	at loci.formats.codec.JPEG2000Codec.decompress(JPEG2000Codec.java:63)
	at loci.formats.in.DicomReader.getTile(DicomReader.java:1622)
	at loci.formats.in.DicomReader.openBytes(DicomReader.java:304)
	at loci.formats.ImageReader.openBytes(ImageReader.java:467)
	at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:169)
	at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:161)
	at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:202)
	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:350)
	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:350)
	at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:269)

…used This makes sure that the tiles actually saved match the tile sizes supplied to the writer.

melissalinkert · 2024-06-26T22:59:53Z

Loading the generated DICOM files into OMERO for visual assessment and comparison to the original, all datasets worked as expected with the exception of the DICOM dataset created from the SVS file using -precompressed and -compression JPEG-2000 as the import failed with

In this case the pyramid is converted tile-wise, but the extra images are not, which was a problem since the reader's optimal tile sizes are now sent to the writer any time -precompressed is used. I think 4f2a96e is one way to fix, but open to other thoughts.

imagesc-bot · 2024-06-27T12:30:19Z

This pull request has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/file-format-to-store-images-using-ngff-coverter/98320/4

sbesson

Retested with the last commit. The conversion times are identical to the ones reported previously and all images including the label images are now viewable

dgault

The actual code changes look good from my side and moving the logic to MinimalTiffReader makes sense.

I tested some conversions from images at https://downloads.openmicroscopy.org/images/Hamamatsu-NDPI/openslide/ to DICOM, with and without the new option. Similar to Seb's finding, the conversions were all successful and images opened and displayed as expected. I also saw similar speed up times as mentioned above when converting with the precompressed option.

melissalinkert added 6 commits April 4, 2024 16:15

Update JPEGTurboService to return compressed tiles, tile dimensions

c1c59a0

NDPI: first version of precompressed tile reading

32c9fec

Fix interpretation of x and y coordinates

41eb29e

Refactor generic TIFF tile logic

e21ed51

DICOM writer: allow different tile sizes for each resolution

b78a93f

This provides better precompressed tile support for input formats that don't have a constant tile size across all resolutions.

NDPI: fix tile size and precompressed tile reading for extra images

b94bed3

melissalinkert added the exclude label Apr 12, 2024

melissalinkert added this to the 8.0.0 milestone Apr 12, 2024

melissalinkert mentioned this pull request May 23, 2024

Extend precompressed support to read DICOM and write TIFF/OME-TIFF #4190

Merged

melissalinkert removed the exclude label Jun 13, 2024

melissalinkert requested a review from sbesson June 13, 2024 19:27

sbesson requested changes Jun 20, 2024

View reviewed changes

Fix tile size/count writing when calling saveBytes

23780de

sbesson requested changes Jun 24, 2024

View reviewed changes

bfconvert: convert DICOM data tile-wise any time -precompressed is …

4f2a96e

…used This makes sure that the tiles actually saved match the tile sizes supplied to the writer.

melissalinkert requested a review from sbesson June 26, 2024 23:02

sbesson approved these changes Jul 2, 2024

View reviewed changes

dgault approved these changes Jul 22, 2024

View reviewed changes

dgault merged commit 678fd01 into ome:develop Jul 22, 2024
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melissalinkert deleted the ndpi-precompressed branch September 6, 2024 19:00

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Add support for reading compressed NDPI tiles #4181

Add support for reading compressed NDPI tiles #4181

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Add support for reading compressed NDPI tiles #4181

Add support for reading compressed NDPI tiles #4181

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