Fix class cast and labels issue. #98

dominikl · 2024-10-28T13:45:11Z

This PR should fix two issues:

If I create an ome.zarr with labels and omero section in .zattr, I get an ClassCastException:

2024-10-28 13:26:24,834 16832      [      main] ERROR     ome.formats.importer.cli.ErrorHandler - FILE_EXCEPTION: /test/tile_5_with_labels.ome.zarr/2/0/2/25/0/0
java.lang.ClassCastException: class java.lang.Integer cannot be cast to class java.lang.Double (java.lang.Integer and java.lang.Double are in module java.base of loader 'bootstrap')
        at loci.formats.in.ZarrReader.parseOmeroMetadata(ZarrReader.java:933)
        at loci.formats.in.ZarrReader.initFile(ZarrReader.java:208)
        at loci.formats.FormatReader.setId(FormatReader.java:1480)

And indeed in the respective line of .zattr

"coefficient" : 1,

It's an integer.

With this PR an Integer gets properly casted into the Double.

If the ome.zarr name contains the String "labels" all files will be skipped.

dominikl · 2024-10-30T14:08:24Z

I'll remove Melissa's commits again, once her PR #97 is merged.

dominikl · 2024-10-30T14:11:51Z

Showinf now works with ome.zarrs with "label" in the name. Unfortunately I still can't import them (still no imports), but now I'm really at the end my flagpole (how I'd say in German).

sbesson

From a strict code review perspective, the proposed changes look sensible and should relax the coefficient parsing as well as the exclusion of any Zarr dataset containing labels in its name.

What is the plan for testing this functionality? Should this be tested using the Bio-Formats command-line utilities?
Otherwise, the overarching question for the IDR team is what is the testing plan for evaluating these changes in the context of an IDR deployment. Should this be deployed on a pilot/idr-testing? Is it expected that memo files will be unmodified? /cc @will-moore @francesw @jburel

dominikl · 2024-11-04T12:35:37Z

Rebased, won't include Melissas bioformats update commit for now.

dominikl · 2024-11-06T13:27:45Z

How to test

'labels' issue

Create an ome.zarr with bioformats2raw.

Check it with showinf and ZarrReader 0.5.2:

BF_CP=OMEZarrReader-0.5.2-jar-with-dependencies.jar showinf -nopix A-Cat.ome.zarr/.zattrs

You'll see the used files list:

Used files:
	/Users/dom/Testing/zarr/A-Cat.ome.zarr/.zattrs
	/Users/dom/Testing/zarr/A-Cat.ome.zarr/.zgroup
	...

Change the ome.zarr name to include 'labels', e.g.
mv A-Cat.ome.zarr A-Cat_labels.ome.zarr

Run again:
BF_CP=OMEZarrReader-0.5.2-jar-with-dependencies.jar showinf -nopix A-Cat_labels.ome.zarr/.zattrs

Now you'll get:

************ invalid used files list ************
Used files = []

(use in omero this will lead to "no imports found")

Then use the jar from this PR:

BF_CP=OMEZarrReader-0.5.3-SNAPSHOT-jar-with-dependencies.jar showinf -nopix A-Cat_labels.ome.zarr/.zattrs

Used files:
	/Users/dom/Testing/zarr/A-Cat_labels.ome.zarr/.zattrs
	/Users/dom/Testing/zarr/A-Cat_labels.ome.zarr/.zgroup
	...

Class cast issue

For some reason the 'omero' metadata is only read when it is part of the root dir,
i.e. A-Cat.ome.zarr/.zattrs. But bioformats2raw adds everything to a 'series' 0 directory.
So you have to 'flatten' it, ie. move everything in A-Cat.ome.zarr/0 one level up into the
root dir A-Cat.ome.zarr (including the .zattr and .zgroup files!)
Then run:
BF_CP=OMEZarrReader-0.5.2-jar-with-dependencies.jar showinf A-Cat.ome.zarr/.zattrs

Get:

Exception in thread "main" java.lang.ClassCastException: class java.lang.Integer cannot be cast to class java.lang.Double (java.lang.Integer and java.lang.Double are in module java.base of loader 'bootstrap')
	at loci.formats.in.ZarrReader.parseOmeroMetadata(ZarrReader.java:933)
	...

With the ZarrReader from the PR:
BF_CP=OMEZarrReader-0.5.3-SNAPSHOT-jar-with-dependencies.jar showinf A-Cat.ome.zarr/.zattrs
Works as expected.

sbesson

Using bioformats2raw 0.9.4, I created two synthetic examples labels_example.zarr and labels_example_flattened.zarr.

With the Bio-Formats 7.3.1 command-line tools and ZarrReader 0.5.2 (built from the tag)

sbesson@Sebastiens-MacBook-Pro-3 ZarrReader % BF_CP=./target/OMEZarrReader-0.5.2-jar-with-dependencies.jar ~/Downloads/bftools/showinf ~/Downloads/labels_example.zarr/.zattrs -noflat
Checking file format [Zarr]
Initializing reader
ZarrReader initializing /Users/sbesson/Downloads/labels_example.zarr/.zattrs
Mismatch with group key paths and original OME-XML metadata, original ordering wont be maintained
Initialization took 0.309s

Reading core metadata
filename = /Users/sbesson/Downloads/labels_example.zarr/.zattrs
************ invalid used files list ************
Used files = []
Series count = 1
Series #0 :
	Resolutions = 4
		sizeX[0] = 2000
		sizeX[1] = 1000
		sizeX[2] = 500
		sizeX[3] = 250
	Image count = 30
	RGB = false (1) 
	Interleaved = false
	Indexed = false (false color)
	Width = 2000
	Height = 2000
	SizeZ = 10
	SizeT = 1
	SizeC = 3
	Tile size = 250 x 250
	Thumbnail size = 128 x 128
	Endianness = intel (little)
	Dimension order = XYZCT (uncertain)
	Pixel type = uint8
	Valid bits per pixel = 8
	Metadata complete = false
	Thumbnail series = false
	-----
	Plane #0 <=> Z 0, C 0, T 0
	Plane #13 <=> Z 3, C 1, T 0
	Plane #14 <=> Z 4, C 1, T 0
	Plane #15 <=> Z 5, C 1, T 0
	Plane #16 <=> Z 6, C 1, T 0
	Plane #17 <=> Z 7, C 1, T 0
	Plane #29 <=> Z 9, C 2, T 0


Reading pixel data (0-29)
	Read 23/30 planes (76%)
	Read 30/30 planes (100%)
[done]
1.152s elapsed (38.4ms per plane)

Launching image viewer

Reading global metadata
Axis name:0:0: t
Axis name:0:1: c
Axis name:0:2: z
Axis name:0:3: y
Axis name:0:4: x
Axis type:0:0: time
Axis type:0:1: channel
Axis type:0:2: space
Axis type:0:3: space
Axis type:0:4: space

Reading metadata
^C%                                                                                                                                                                                  sbesson@Sebastiens-MacBook-Pro-3 ZarrReader % BF_CP=./target/OMEZarrReader-0.5.2-jar-with-dependencies.jar ~/Downloads/bftools/showinf ~/Downloads/labels_example_flattened.zarr/.zattrs -noflat
Checking file format [Zarr]
Initializing reader
ZarrReader initializing /Users/sbesson/Downloads/labels_example_flattened.zarr/.zattrs
Exception in thread "main" java.lang.ClassCastException: class java.lang.Integer cannot be cast to class java.lang.Double (java.lang.Integer and java.lang.Double are in module java.base of loader 'bootstrap')
	at loci.formats.in.ZarrReader.parseOmeroMetadata(ZarrReader.java:933)
	at loci.formats.in.ZarrReader.initFile(ZarrReader.java:208)
	at loci.formats.FormatReader.setId(FormatReader.java:1480)
	at loci.formats.ImageReader.setId(ImageReader.java:864)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)
	at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:1043)
	at loci.formats.tools.ImageInfo.main(ImageInfo.java:1129)

With this PR

sbesson@Sebastiens-MacBook-Pro-3 ZarrReader % BF_CP=./target/OMEZarrReader-0.5.3-SNAPSHOT-jar-with-dependencies.jar ~/Downloads/bftools/showinf ~/Downloads/labels_example.zarr/.zattrs -noflat 
Checking file format [Zarr]
Initializing reader
ZarrReader initializing /Users/sbesson/Downloads/labels_example.zarr/.zattrs
Mismatch with group key paths and original OME-XML metadata, original ordering wont be maintained
Initialization took 0.307s

Reading core metadata
filename = /Users/sbesson/Downloads/labels_example.zarr/.zattrs
Used files:
	/Users/sbesson/Downloads/labels_example.zarr/.DS_Store
	/Users/sbesson/Downloads/labels_example.zarr/.zattrs
	/Users/sbesson/Downloads/labels_example.zarr/.zgroup
	/Users/sbesson/Downloads/labels_example.zarr/0/.zattrs
	/Users/sbesson/Downloads/labels_example.zarr/0/.zgroup
	/Users/sbesson/Downloads/labels_example.zarr/0/0/.zarray
	/Users/sbesson/Downloads/labels_example.zarr/0/0/0/0/9/0/0
	/Users/sbesson/Downloads/labels_example.zarr/0/0/0/0/9/0/1
	/Users/sbesson/Downloads/labels_example.zarr/0/0/0/0/9/1/0
	/Users/sbesson/Downloads/labels_example.zarr/0/0/0/0/9/1/1
	/Users/sbesson/Downloads/labels_example.zarr/0/0/0/0/0/0/0
	/Users/sbesson/Downloads/labels_example.zarr/0/0/0/0/0/0/1
	/Users/sbesson/Downloads/labels_example.zarr/0/0/0/0/0/1/0
	/Users/sbesson/Downloads/labels_example.zarr/0/0/0/0/0/1/1
	/Users/sbesson/Downloads/labels_example.zarr/0/0/0/0/7/0/0
	/Users/sbesson/Downloads/labels_example.zarr/0/0/0/0/7/0/1
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	/Users/sbesson/Downloads/labels_example.zarr/0/0/0/0/7/1/1
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	/Users/sbesson/Downloads/labels_example.zarr/0/0/0/2/5/1/1
	/Users/sbesson/Downloads/labels_example.zarr/0/1/.zarray
	/Users/sbesson/Downloads/labels_example.zarr/0/1/0/0/9/0/0
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	/Users/sbesson/Downloads/labels_example.zarr/0/3/.zarray
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	/Users/sbesson/Downloads/labels_example.zarr/OME/METADATA.ome.xml
	/Users/sbesson/Downloads/labels_example.zarr/OME/.zattrs
	/Users/sbesson/Downloads/labels_example.zarr/OME/.zgroup
Series count = 1
Series #0 :
	Resolutions = 4
		sizeX[0] = 2000
		sizeX[1] = 1000
		sizeX[2] = 500
		sizeX[3] = 250
	Image count = 30
	RGB = false (1) 
	Interleaved = false
	Indexed = false (false color)
	Width = 2000
	Height = 2000
	SizeZ = 10
	SizeT = 1
	SizeC = 3
	Tile size = 250 x 250
	Thumbnail size = 128 x 128
	Endianness = intel (little)
	Dimension order = XYZCT (uncertain)
	Pixel type = uint8
	Valid bits per pixel = 8
	Metadata complete = false
	Thumbnail series = false
	-----
	Plane #0 <=> Z 0, C 0, T 0
	Plane #13 <=> Z 3, C 1, T 0
	Plane #14 <=> Z 4, C 1, T 0
	Plane #15 <=> Z 5, C 1, T 0
	Plane #16 <=> Z 6, C 1, T 0
	Plane #17 <=> Z 7, C 1, T 0
	Plane #29 <=> Z 9, C 2, T 0


Reading pixel data (0-29)
	Read 26/30 planes (86%)
	Read 30/30 planes (100%)
[done]
1.103s elapsed (36.766666ms per plane)

Launching image viewer

Reading global metadata
Axis name:0:0: t
Axis name:0:1: c
Axis name:0:2: z
Axis name:0:3: y
Axis name:0:4: x
Axis type:0:0: time
Axis type:0:1: channel
Axis type:0:2: space
Axis type:0:3: space
Axis type:0:4: space

Reading metadata
^C%                                                                                                                                                                                  sbesson@Sebastiens-MacBook-Pro-3 ZarrReader % BF_CP=./target/OMEZarrReader-0.5.3-SNAPSHOT-jar-with-dependencies.jar ~/Downloads/bftools/showinf ~/Downloads/labels_example_flattened.zarr/.zattrs -noflat
Checking file format [Zarr]
Initializing reader
ZarrReader initializing /Users/sbesson/Downloads/labels_example_flattened.zarr/.zattrs
Mismatch with group key paths and original OME-XML metadata, original ordering wont be maintained
Initialization took 0.239s

Reading core metadata
filename = /Users/sbesson/Downloads/labels_example_flattened.zarr/.zattrs
Used files:
	/Users/sbesson/Downloads/labels_example_flattened.zarr/.DS_Store
	/Users/sbesson/Downloads/labels_example_flattened.zarr/.zattrs
	/Users/sbesson/Downloads/labels_example_flattened.zarr/.zgroup
	/Users/sbesson/Downloads/labels_example_flattened.zarr/0/.zarray
	/Users/sbesson/Downloads/labels_example_flattened.zarr/0/0/0/9/0/0
	/Users/sbesson/Downloads/labels_example_flattened.zarr/0/0/0/9/0/1
	/Users/sbesson/Downloads/labels_example_flattened.zarr/0/0/0/9/1/0
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Series count = 1
Series #0 :
	Resolutions = 4
		sizeX[0] = 2000
		sizeX[1] = 1000
		sizeX[2] = 500
		sizeX[3] = 250
	Image count = 30
	RGB = false (1) 
	Interleaved = false
	Indexed = false (false color)
	Width = 2000
	Height = 2000
	SizeZ = 10
	SizeT = 1
	SizeC = 3
	Tile size = 250 x 250
	Thumbnail size = 128 x 128
	Endianness = intel (little)
	Dimension order = XYZCT (uncertain)
	Pixel type = uint8
	Valid bits per pixel = 8
	Metadata complete = false
	Thumbnail series = false
	-----
	Plane #0 <=> Z 0, C 0, T 0
	Plane #13 <=> Z 3, C 1, T 0
	Plane #14 <=> Z 4, C 1, T 0
	Plane #15 <=> Z 5, C 1, T 0
	Plane #16 <=> Z 6, C 1, T 0
	Plane #17 <=> Z 7, C 1, T 0
	Plane #29 <=> Z 9, C 2, T 0


Reading pixel data (0-29)
	Read 26/30 planes (86%)
	Read 30/30 planes (100%)
[done]
1.094s elapsed (36.466667ms per plane)

Launching image viewer

Reading global metadata
Axis name:0:0: t
Axis name:0:1: c
Axis name:0:2: z
Axis name:0:3: y
Axis name:0:4: x
Axis type:0:0: time
Axis type:0:1: channel
Axis type:0:2: space
Axis type:0:3: space
Axis type:0:4: space

Reading metadata
^C%

sbesson · 2024-11-07T10:57:54Z

src/loci/formats/in/ZarrReader.java

@@ -930,7 +925,9 @@ private void parseOmeroMetadata(String root, Map<String, Object> attr) throws IO
      for (int i = 0; i < channels.size(); i++) {
        Map<String, Object> channel = (Map<String, Object>) channels.get(i);
        Boolean channelActive = (Boolean) channel.get("active");
-        Double channelCoefficient = (Double) channel.get("coefficient");
+        Double channelCoefficient = channel.get("coefficient") instanceof Double ?


See also #95 an alternative to the intanceof check would be to read these as Number

Ah thanks, so that actually already has been fixed in another PR, should have checked properly. Maybe we could merge the other PR first...

Only obvious caveat is that #95 needs additional work to get the test to compile first. But if that was the preferred option, no objection from my side to splitting these fixes into 2 separate PRs.

dominikl · 2024-12-05T14:57:02Z

Close in favor of #100. But I think @sbesson review is also still valid for #100 .

dominikl force-pushed the fix_channel_coeff_cast branch from cb14280 to b2c2b9c Compare October 29, 2024 14:54

dominikl marked this pull request as draft October 30, 2024 10:29

dominikl force-pushed the fix_channel_coeff_cast branch from b2c2b9c to 2523f33 Compare October 30, 2024 14:04

dominikl marked this pull request as ready for review October 30, 2024 14:06

dominikl requested a review from sbesson October 30, 2024 14:11

sbesson reviewed Oct 30, 2024

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melissalinkert and others added 3 commits November 4, 2024 12:25

Update all actions to v4

3b3cda8

Channel coeff can be Integer or Double

0adcd0b

Fix issue if 'labels' part of filename

6a2f882

dominikl force-pushed the fix_channel_coeff_cast branch from 2523f33 to 6a2f882 Compare November 4, 2024 12:25

dominikl changed the title ~~Channel coeff can be Integer or Double~~ Fix class cast and labels issue. Nov 6, 2024

sbesson approved these changes Nov 7, 2024

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sbesson requested a review from will-moore November 7, 2024 10:55

sbesson reviewed Nov 7, 2024

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dominikl mentioned this pull request Dec 5, 2024

Fix issues #100

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Fix class cast and labels issue. #98

Fix class cast and labels issue. #98

dominikl commented Oct 28, 2024 •

edited

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dominikl commented Dec 5, 2024

Fix class cast and labels issue. #98

Fix class cast and labels issue. #98

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dominikl commented Oct 28, 2024 • edited Loading

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dominikl commented Nov 6, 2024

How to test

'labels' issue

Class cast issue

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dominikl commented Oct 28, 2024 •

edited

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