Ticket #514 (closed defect: fixed)

Opened 9 years ago

Last modified 9 years ago

Fix Image5D and View5D view modes

Reported by: curtis Owned by: curtis
Priority: minor Milestone: bio-formats-4.2.1
Component: plugins Severity: serious
Keywords: Cc:
Blocked By: Blocking:

Description

There may be an issue with Image5D and View5D view modes, as they were not well-tested before the 4.2 release. Investigate, and make sure they work.

Relevant code is in the displayImage5D and displayView5D methods of source:trunk/components/loci-plugins/src/loci/plugins/in/DisplayHandler.java.

Attachments

image5d-z-slider.diff Download (163 bytes) - added by melissa 9 years ago.

Change History

comment:1 Changed 9 years ago by melissa

(In [6701]) Fixed View5D instantiation; see #514.

comment:2 follow-ups: ↓ 5 ↓ 7 Changed 9 years ago by melissa

Remaining Image5D issues:

  • Z slider doesn't work (tested against andor/mark/MF-2CH-Z-T.tif). The play/pause button, however, does work.
  • An exception is thrown if the "concatenate series" option is checked (tested against andor/mark/MF-2CH-Z-T.tif). Most likely, we want to disable this option if the Image5D display mode is selected.
  • An exception is thrown when trying to open a subset of planes.

Remaining View5D issues:

  • View5D prompts for image dimensions (tested against andor/mark/VESSEL-DEC-Z.tif). I don't know what (if anything) we can do about this, but it's kind of annoying given that the original ImagePlus contains all of the dimension information.

comment:3 follow-up: ↓ 4 Changed 9 years ago by melissa

(In [6703]) Disable the "concatenate series" option when displaying with Image5D. See #514.

comment:4 in reply to: ↑ 3 Changed 9 years ago by curtis

Replying to melissa:

(In [6703]) Disable the "concatenate series" option when displaying with Image5D. See #514.

It is not clear to me why this should be necessary. The resultant ImagePlus object (after concatenation) should be no different than any other ImagePlus, so why wouldn't it be displayable within Image5D?

comment:5 in reply to: ↑ 2 Changed 9 years ago by curtis

Remaining View5D issues:

  • View5D prompts for image dimensions (tested against andor/mark/VESSEL-DEC-Z.tif). I don't know what (if anything) we can do about this, but it's kind of annoying given that the original ImagePlus contains all of the dimension information.

I thought we had found a way around this before. Perhaps a different View5D constructor? At worst, we can email the author asking for a way to avoid it.

comment:6 Changed 9 years ago by melissa

(In [6704]) * Reverted r6703 stupidity.

  • Fixed Image5D display mode to work with concatenation and range options; see #514.

comment:7 in reply to: ↑ 2 Changed 9 years ago by melissa

Replying to melissa:

Remaining Image5D issues:

  • Z slider doesn't work (tested against andor/mark/MF-2CH-Z-T.tif). The play/pause button, however, does work.

This is a bug in Image5D; the attached patch solves it.

Changed 9 years ago by melissa

comment:8 Changed 9 years ago by curtis

  • Owner changed from melissa to curtis

The remaining work for Image5D is to apply Melissa's patch to the Image5D codebase, posting the updated version to our web site, and notifying interested parties.

For View5D, we should dig a little more to eliminate the need to respecify the image dimensions, since they are already known (and I think this used to work).

comment:9 Changed 9 years ago by curtis

I have set up  Image5D in the ImageJDev.org codebase, added an  Image5D page to the web site,  committed Melissa's patch, and  released Image5D 1.2.1.

All that remains to close this ticket is to eliminate the extra View5D dialog.

comment:10 Changed 9 years ago by curtis

  • Status changed from new to closed
  • Resolution set to fixed

I reviewed the View5D code, and there is simply no way to avoid invoking a dialog pop-up when calling the View5D_ constructor with multidimensional data. So I'm going to punt on the extra View5D dialog for now—if people complain, we can contact the View5D author to resolve it.

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