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Imagej prep #3329

Merged
merged 61 commits into from
Jan 30, 2015
Merged

Imagej prep #3329

merged 61 commits into from
Jan 30, 2015

Commits on Dec 19, 2014

  1. Initial clean up.

    @jburel
    jburel committed Dec 19, 2014
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  2. Adjust container so correct agent is activated.

    @jburel
    jburel committed Dec 19, 2014
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Commits on Jan 12, 2015

  1. Do not invoke shutdown twice when run as a plugin.

    @jburel
    jburel committed Jan 12, 2015
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  2. Remove import and add doc.

    @jburel
    jburel committed Jan 12, 2015
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  3. Fix terminate method.

    @jburel
    jburel committed Jan 12, 2015
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  4. remove imports.

    @jburel
    jburel committed Jan 12, 2015
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  5. Add option to import images from ImageJ

    @jburel
    jburel committed Jan 12, 2015
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  6. Modify text to match mock-up.

    @jburel
    jburel committed Jan 12, 2015
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  7. Remove imports

    @jburel
    jburel committed Jan 12, 2015
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  8. Modify init sequence of agents when use as plugin.

    @jburel
    jburel committed Jan 12, 2015
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  9. Update header and remove import introduced while debugging.

    @jburel
    jburel committed Jan 12, 2015
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  10. Refactor code to handle imagePlus object.

    @jburel
    jburel committed Jan 12, 2015
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  11. Fix possible NPE.

    @jburel
    jburel committed Jan 12, 2015
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  12. Add docs

    @jburel
    jburel committed Jan 12, 2015
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  13. Generate ome.tiff if image is modified.

    @jburel
    jburel committed Jan 12, 2015
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  14. Add compression parameter

    @jburel
    jburel committed Jan 12, 2015
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  15. Pass lower case parameter.

    @jburel
    jburel committed Jan 12, 2015
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  16. Remove commented out code.

    @jburel
    jburel committed Jan 12, 2015
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  17. Review way to specify parameter

    @jburel
    jburel committed Jan 12, 2015
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  18. Rename tmp file.

    @jburel
    jburel committed Jan 12, 2015
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  19. Fix possible NPE while adding listeners.

    @jburel
    jburel committed Jan 12, 2015
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  20. Rename file as ome.tif.

    @jburel
    jburel committed Jan 12, 2015
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  21. Review delete sequence.

    @jburel
    jburel committed Jan 12, 2015
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  22. Review agents loading sequence.

    @jburel
    jburel committed Jan 12, 2015
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  23. Use collectionUtils.

    @jburel
    jburel committed Jan 12, 2015
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  24. Handle whitespace path.

    @jburel
    jburel committed Jan 12, 2015
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  25. Remove extension and set path to name.

    @jburel
    jburel committed Jan 12, 2015
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Commits on Jan 13, 2015

  1. toString() method uses the original file.

    @jburel
    jburel committed Jan 13, 2015
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  2. Add message.

    @jburel
    jburel committed Jan 13, 2015
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  3. Add option to import as orphaned.

    @jburel
    jburel committed Jan 13, 2015
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  4. Handle file with space in name.

    @jburel
    jburel committed Jan 13, 2015
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  5. Fix possible NPE.

    @jburel
    jburel committed Jan 13, 2015
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  6. Fix typo.

    @jburel
    jburel committed Jan 13, 2015
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  7. Fix possible NPE if no log id returned.

    @jburel
    jburel committed Jan 13, 2015
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  8. Initial work to support roi.

    @jburel
    jburel committed Jan 13, 2015
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Commits on Jan 14, 2015

  1. read more shape types.

    @jburel
    jburel committed Jan 14, 2015
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  2. Remove imports

    @jburel
    jburel committed Jan 14, 2015
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  3. Update ij.jar to match version in B-F

    @jburel
    jburel committed Jan 14, 2015
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  4. Add support for all roi types.

    @jburel
    jburel committed Jan 14, 2015
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  5. Open image in ImageJ when in import mode.

    @jburel
    jburel committed Jan 14, 2015
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  6. Add support for roi settings.

    @jburel
    jburel committed Jan 14, 2015
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  7. clean up.

    @jburel
    jburel committed Jan 14, 2015
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Commits on Jan 15, 2015

  1. Add option to import current image or all images.

    @jburel
    jburel committed Jan 15, 2015
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  2. Read from overlay

    @jburel
    jburel committed Jan 15, 2015
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Commits on Jan 16, 2015

  1. Add image from manager if no overlay

    @jburel
    jburel committed Jan 16, 2015
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  2. Remove not required IJ.log

    @jburel
    jburel committed Jan 16, 2015
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  3. Fix display when importer opened from data manager.

    @jburel
    jburel committed Jan 16, 2015
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  4. Add Save to OMERO to File>Import

    @jburel
    jburel committed Jan 16, 2015
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  5. Fix default dataset depending on context.

    @jburel
    jburel committed Jan 16, 2015
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  6. Fix entry in File menu.

    @jburel
    jburel committed Jan 16, 2015
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Commits on Jan 19, 2015

  1. Fix menu entry.

    @jburel
    jburel committed Jan 19, 2015
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Commits on Jan 20, 2015

  1. Fix import and reading of tiff files.

    @jburel
    jburel committed Jan 20, 2015
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  2. Fix text as suggested by Petr.

    @jburel
    jburel committed Jan 20, 2015
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Commits on Jan 21, 2015

  1. Remove imports

    @jburel
    jburel committed Jan 21, 2015
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  2. Handle addition of MIF to queue.

    @jburel
    jburel committed Jan 21, 2015
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Commits on Jan 22, 2015

  1. Pass imageID to plugin

    @jburel
    jburel committed Jan 22, 2015
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  2. Fix NPE if quit is pressed from login screen.

    @jburel
    jburel committed Jan 22, 2015
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Commits on Jan 26, 2015

  1. Prepare to save overlay on images from MIF.

    @jburel
    jburel committed Jan 26, 2015
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Commits on Jan 27, 2015

  1. Improve support for MIF and overlay.

    @jburel
    jburel committed Jan 27, 2015
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  2. Review reading of roi from manager.

    @jburel
    jburel committed Jan 27, 2015
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  3. Fix connect after quit 

    Quit application before connecting was leading to
agent not showing up.
    @jburel
    jburel committed Jan 27, 2015
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