Ticket #1457 (new feature)

Opened 6 years ago

Last modified 5 years ago

Fix obviously failing commands [analysis]

Reported by: bdezonia Owned by: bdezonia
Priority: major Milestone: imagej2-b8-analysis
Component: Core Version:
Severity: serious Keywords:
Cc: Blocked By: #1313, #1336, #1431, #1433, #1605, #1756, #1769, #1813, #1841, #1852, #1856, #1881, #1888, #1903, #1904, #1908, #1910, #1922, #1930, #1948, #1958, #1961, #1964, #1966, #1972, #1973, #1981, #1986, #1990, #1992, #1993, #1994, #1995, #2002, #2005, #2006, #2008, #2014, #2015, #2019, #2020, #2022, #2028, #2029
Blocking:

Description

Some commands in IJ2 fail in a very apparent fashion. They should be addressed preferentially. See blockers to this ticket.

Change History

comment:1 Changed 6 years ago by bdezonia

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comment:13 Changed 6 years ago by bdezonia

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comment:14 Changed 6 years ago by curtis

  • Milestone changed from imagej-2.0.0-beta6 to imagej-2.0.0-beta7

comment:15 Changed 6 years ago by curtis

  • Summary changed from Fix obviously failing commands (2.0.0-beta5) to Fix obviously failing commands (2.0.0-beta7)

comment:16 Changed 6 years ago by bdezonia

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comment:21 Changed 6 years ago by bdezonia

  • Summary changed from Fix obviously failing commands (2.0.0-beta7) to Fix obviously failing commands (2.0.0-beta8)

comment:22 Changed 6 years ago by bdezonia

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comment:23 Changed 6 years ago by curtis

  • Summary changed from Fix obviously failing commands (2.0.0-beta8) to Fix obviously failing commands [analysis]

comment:24 Changed 6 years ago by bdezonia

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comment:27 Changed 5 years ago by bdezonia

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comment:28 Changed 5 years ago by bdezonia

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(In #1880) This issue no longer apparent on the scifio-cells branch (soon to be merged)

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comment:38 Changed 5 years ago by bdezonia

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(In #1881) Note that scifio-cells has been merged to master.

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comment:40 Changed 5 years ago by bdezonia

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comment:41 Changed 5 years ago by hinerm

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(In #1908) Currently, these images are opened similarly using SCIFIO as in FIJI with the Bio-Formats importer.

In both cases, they are opened as RGBA. Compositing the alpha channel makes the images look off.

IJ1 seems to be taking extra steps to process the alpha channel out, and opens this as an RGB image instead.

So we need to decide how to handle alpha channels.

Also, the color table for the 4th channel is blue in IJ2 but the Bio-Formats importer and IJ1 use white.

comment:42 Changed 5 years ago by bdezonia

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comment:46 Changed 5 years ago by bdezonia

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(In #1960) This is an issue where the SwingInputHarvester assumes you'll never update any attributes of an existing dialog. The SwingInputHarvester could be modified so that it tied together the Module and the SwingDialog. Thus a Module would be able to update the SwingDialog when its title changes (for example). Deferring this ticket to a later beta. In the meantime I have disabled title setting code in HistogramPlot with a note explaining why.

comment:47 Changed 5 years ago by bdezonia

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comment:54 Changed 5 years ago by curtis

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(In #1946) This seems like a situation where the synchronizer needs to be smart about the limitations of IJ1. If the IJ2 version of the image has multiple distinct color tables, then it should certainly not overwrite all of them with the ImageJ1 color table. It would be ideal if the ImageJ1 color table could somehow be tied to the "correct" color table in ImageJ2, and then only that one would get synchronized in case of changes in ImageJ1-land. The simplest approach would be to always use the first color table of the IJ2 image for this.

In the case of the image being restructured, it becomes less clear how to maintain this mapping. But for the workflow above, no restructuring takes place—pixel values are merely zeroed out. So it might work.

However, there are many other potential compatibility issues, even if we were to employ this strategy. Because in ImageJ1-land, as you say, the color table *is* only red, and anyone expecting things being otherwise (based on their perception from the modern UI) will be disappointed.

Booting this ticket to imagej2-b10-compatibility, since we have bigger fish to fry.

comment:55 Changed 5 years ago by bdezonia

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