Skip to content
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
54 commits
Select commit Hold shift + click to select a range
b9aac67
Simplify `getClass().toString()` to `getClass()` in log messages.
stefanhahmann Feb 19, 2026
c4d1d62
Add more logging for dataset properties in `OpenInBDVCommand`
stefanhahmann Feb 19, 2026
f35e5ba
Update plugin annotation to include menu path in `OpenInBDVCommand`
stefanhahmann Feb 19, 2026
7bf4a6d
Add custom exceptions for single-scale and multiscale image validatio…
stefanhahmann Feb 20, 2026
6e0bcf9
Change image-opening logic to support both single-scale and multiscal…
stefanhahmann Feb 20, 2026
ee2862e
Allow instantiation of DefaultPyramidal5DImageData without MultiScale…
stefanhahmann Feb 20, 2026
7f2af16
Add `getPyramidName` method to `PyramidalDataset` for retrieving data…
stefanhahmann Feb 20, 2026
c374782
Initialize `SharedQueue` in `MultiscaleImage` constructor with dynami…
stefanhahmann Feb 20, 2026
6d9a774
Add example path for testing multiscale data in `MultiscaleImageDemo`
stefanhahmann Feb 20, 2026
9831134
Add test for `findImageRootFolder` starting at leave folder
stefanhahmann Feb 20, 2026
b6358b6
Enhance validation for multiscale image paths in `DefaultPyramidal5DI…
stefanhahmann Feb 20, 2026
d9ac1d5
Change plugin menu path capitalization in `OpenInBDVCommand`
stefanhahmann Feb 23, 2026
703a885
Move classes Multiscales, OMEZarrData and MultiscaleImage from produc…
stefanhahmann Feb 23, 2026
1ffa8aa
Extract N5ReaderDemo from DefaultPyramidal5DImageData and move to tes…
stefanhahmann Feb 23, 2026
0e547b8
Remove TODO comments
stefanhahmann Feb 23, 2026
b8b4140
Remove code example regarding importing ImagePlus
stefanhahmann Feb 23, 2026
aaf81a1
Clarify root folder traversal comments and remove TODOs
stefanhahmann Feb 23, 2026
4f30ac0
Refactor `DefaultPyramidal5DImageData` to improve path handling and r…
stefanhahmann Feb 24, 2026
7b7df8f
Mark fields in `DefaultPyramidal5DImageData` as final where applicabl…
stefanhahmann Feb 24, 2026
681451a
Refactor axis configuration and metadata handling in `DefaultPyramida…
stefanhahmann Feb 24, 2026
519b1b1
Simplify type inference by removing redundant generic type argument i…
stefanhahmann Feb 24, 2026
b592f48
Rename `numResolutions` to `numResolutionLevels`
stefanhahmann Feb 24, 2026
7e3daeb
Add test assertion for mipmap levels in `DefaultPyramidal5DImageDataT…
stefanhahmann Feb 24, 2026
915cde5
Update menu path in `OpenInBDVCommand` plugin annotation
stefanhahmann Feb 25, 2026
9366e57
Extract `IMAGE_NAME` constant to `ZarrTestUtils` and update reference…
stefanhahmann Feb 26, 2026
46c5ca1
Add tests regarding datasetservice for opening routes ImageJ and BDV …
stefanhahmann Feb 26, 2026
d236e71
Add `testGetPyramidLevels` to validate resolution levels in `DefaultP…
stefanhahmann Feb 27, 2026
5b3654d
Install libblosc in CI
stefanhahmann Feb 27, 2026
9bcaab7
Re-Format type parameters in `DefaultPyramidal5DImageData` for improv…
stefanhahmann Mar 2, 2026
9c730ff
Remove unused `asSpimData` method and related references from `Pyrami…
stefanhahmann Mar 2, 2026
0d2f9dc
Add metadata format comments for OME NGFF v03/v04 fields in `DefaultP…
stefanhahmann Mar 2, 2026
c519e5b
spimdata
stefanhahmann Mar 2, 2026
ff30c8d
Add JavaDoc for `relativePathAsString` field in `DefaultPyramidal5DIm…
stefanhahmann Mar 2, 2026
d07db7c
Update JavaDoc for `DefaultPyramidal5DImageData` constructor.
stefanhahmann Mar 2, 2026
4fe3265
Simplify `ImgPlus` initialization by combining constructor and name a…
stefanhahmann Mar 2, 2026
76dabb9
Replace `DatasetService` usage with `DefaultDataset` instantiation in…
stefanhahmann Mar 2, 2026
5a3e8a8
Replace `NotAMultiscaleImageException` with `IllegalStateException` i…
stefanhahmann Mar 2, 2026
7d326a7
Update comment for `Selected Scale`
stefanhahmann Mar 2, 2026
25aadbb
Remove unused `SourceAndConverter` import from `DefaultPyramidal5DIma…
stefanhahmann Mar 2, 2026
a259dcd
Use fully qualified name for `OmeNgffMetadata` to replace import.
stefanhahmann Mar 2, 2026
1867472
Rename `configureAxes` to `configureImgPlusAxesFromResolutionLevel`.
stefanhahmann Mar 2, 2026
26cb132
Rename `configureAxes` to `configureImgPlusAxesFromResolutionLevel`.
stefanhahmann Mar 2, 2026
410263e
Add TODO comment to consider caching `PyramidalDataset`
stefanhahmann Mar 2, 2026
f30ab06
Replace `NotAMultiscaleImageException` with `IllegalStateException` i…
stefanhahmann Mar 2, 2026
667dc5d
Remove unrequire imgPlus() method
stefanhahmann Mar 2, 2026
9f0a395
Remove unrequired imgPlus null check
stefanhahmann Mar 2, 2026
238c106
Change code formatting
stefanhahmann Mar 2, 2026
5449001
Change log level 0 (i.e. NONE) to more explicit and better fitting DEBUG
stefanhahmann Mar 2, 2026
9d15e28
Change code formatting
stefanhahmann Mar 2, 2026
da55eec
Do the handling of `NotAMultiscaleImageException` and `NotASingleScal…
stefanhahmann Mar 2, 2026
86d231e
Clarify TODO comments
stefanhahmann Mar 2, 2026
d392e18
Introduce class Multiscale instead of duplicating multiscale properti…
stefanhahmann Mar 2, 2026
872726c
ZarrOpenActions.openBDVWithImage() increases/decreases Dataset usage-…
xulman Mar 3, 2026
84bfaa5
Add comment for `scales` field to indicate it represents the downsamp…
stefanhahmann Mar 4, 2026
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 10 additions & 0 deletions .github/build.sh
Original file line number Diff line number Diff line change
@@ -1,5 +1,15 @@
#!/bin/sh
# Start a virtual X server (Xvfb) on display :99.
# This is required for headless environments (like GitHub CI)
# when running tools that require a graphical display.
export DISPLAY=:99
sudo Xvfb -ac :99 -screen 0 1280x1024x24 > /dev/null 2>&1 &

# Install blosc system library
# Required for building/running code that depends on libblosc.
sudo apt-get update
sudo apt-get install -y libblosc-dev

# Download and execute the SciJava CI build script
curl -fsLO https://raw.githubusercontent.com/scijava/scijava-scripts/main/ci-build.sh
sh ci-build.sh
2 changes: 2 additions & 0 deletions .github/workflows/sonarcloud.yml
Original file line number Diff line number Diff line change
Expand Up @@ -52,6 +52,8 @@ jobs:
run: |
export DISPLAY=:99
sudo Xvfb -ac :99 -screen 0 1280x1024x24 > /dev/null 2>&1 &
sudo apt-get update
sudo apt-get install -y libblosc-dev
mvn -B verify --file pom.xml -Pcoverage sonar:sonar -Dsonar.projectKey=BioImageTools_ome-zarr-fiji-java -Dsonar.organization=bioimagetools

- name: Upload artifacts for subsequent review
Expand Down
Loading