Various minor import fixes #777
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Fixes ticket #11509.
Fixes #11286.
Channels are now detected correctly. If the original file passed to setId is a "d" channel (i.e. original image), then only "d" channels will be included in the used file list. If the file passed to setId is an "o" channel (i.e. analysis results), then only "o" channels will be included in the used file list. Fixes #11148.
For linescans in particular, the Z size is stored in the 'size' field, not the 'start' attribute. Fixes ticket #11513.
This allows datasets with thousands of files to be opened without causing the JVM to run out of file handles. Fixes ticket #10971.
| String well = getWellName(filename); | ||
| int start = well.indexOf(channelCharacter) + 1; | ||
| if (start == 0) { | ||
| start = well.indexOf(channelCharacter) + 1; |
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After importing the 10000 TIFFs into ImageJ (ticket 10971) I don't get an error, but scrolling through the Z sections gives me an "File not found: Frame3_000416.tif" after element number 415. Is this expected? The import finished without the bug described in 10971. |
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For ticket 11513, the dimensions are reported OK: |
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For ticket 11148, the screen imports fine in Insight and no images land in the Orphaned images folder. |
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For ticket 11286, I still get an NPE (FlexReader.java:625) when trying to import the .flex file. Only happens in Fiji though. ImageJ is fine. |
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For 11509, the image scale is reported as 0.74 x 0.74 microns. Seems fine. |
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@melissalinkert All in all, looks good to merge. I couldn't get through testing ticket 11286 in Fiji. Maybe someone else will be better than me at that. |
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@bpindelski: testing PRs in Fiji requires replacing about a dozen different jars and then being careful not to run the updater - dropping loci_tools.jar into the plugins folder isn't going to work. As long as ticket 11286 works in ImageJ, that's sufficient as far as I'm concerned. |
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Also, the "File not found" images for ticket 10971 are expected; those files were exported from somewhere else, and most of the images actually are just plain gray with the text "File not found" and the plane number. |
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@melissalinkert That explains it all then (-: Thanks. |
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Retested importing a Cellomics screen. All looks fine. Good to merge. |
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One more commit added to take care of: http://hudson.openmicroscopy.org.uk/view/Bio-Formats/job/BIOFORMATS-full-repository-develop/553/ |
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Code change looks good and |
Various minor import fixes
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--rebased-to #815 |
To test, verify that builds are green and the issues reported in the following tickets are resolved:
http://trac.openmicroscopy.org.uk/ome/ticket/10971
http://trac.openmicroscopy.org.uk/ome/ticket/11513
http://trac.openmicroscopy.org.uk/ome/ticket/11148
http://trac.openmicroscopy.org.uk/ome/ticket/11265
http://trac.openmicroscopy.org.uk/ome/ticket/11286
http://trac.openmicroscopy.org.uk/ome/ticket/11509