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ImageJ: fix display of composite virtual stacks #1774

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merged 3 commits into from May 6, 2015

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melissalinkert
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Fixes https://trac.openmicroscopy.org/ome/ticket/12267.

To test, use the .czi file from /ome/team/rleigh/lmaier-ij-composite.zip and run the following macro in ImageJ:

run("Bio-Formats Importer", "open=[/path/to/changing colors in composite mode.czi] color_mode=Composite view=Hyperstack stack_order=XYCZT use_virtual_stack");

Without this change, the resulting image window should look OK when initially displayed and each time the Z slider is changed, but the image will change when the C slider is changed (which is not correct for Composite mode).

With this change, adjusting the C slider should not cause the image to change. This should only affect virtual stacks; it might be worth spot checking a few other multi-channel files with Composite mode and virtual stacks enabled.

In testing this, I noticed that the committed ImageJ jar was 1.45s, while the POM specifies 1.48s; c9bb5b4 updates the jar to 1.48s.

@melissalinkert
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Discussed with @bramalingam; there was one more bug where the initial coloring was incorrect. It took me a couple of tries, but this seemed to reliably reproduce the issue:

  • run the macro
  • adjust the C slider to anything other than C=1
  • close the image window
  • without restarting ImageJ, run the macro again and observe that the coloring is different from before

and 819a947 should resolve it.

@bramalingam
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Everything looks good now. Please merge.

melissalinkert added a commit that referenced this pull request May 6, 2015
ImageJ: fix display of composite virtual stacks
@melissalinkert melissalinkert merged commit 2783f06 into ome:develop May 6, 2015
@joshmoore joshmoore added this to the 5.1.2 milestone May 27, 2015
@melissalinkert melissalinkert deleted the 12267 branch January 28, 2016 17:51
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3 participants