User Story #3701 (closed)
Opened 13 years ago
Closed 13 years ago
Update ImportCandidates and Bio-Formats to handle single LSM files
Reported by: | bwzloranger | Owned by: | wmoore |
---|---|---|---|
Priority: | major | Milestone: | OMERO-Beta4.3 |
Component: | Import | Keywords: | n.a. |
Cc: | cxallan, mlinkert, wmoore | Story Points: | n.a. |
Sprint: | 2011-06-16 (14) | Importance: | n.a. |
Total Remaining Time: | n.a. | Estimated Remaining Time: | n.a. |
Description (last modified by cxallan)
Currently, the importer will try to import all LSM files attached to a .mdb file if any of the files are selected and imported. This behaviour should be changed in Bio-Formats so that single LSM files will import if they are selected without the .mdb file. Furthermore, ImportCandidates? should be run whenever LSM or MDB files are selected to get the lowest common denominator set of files to import.
Change History (13)
comment:1 Changed 13 years ago by cxallan
- Cc mlinkert-x wmoore added
- Description modified (diff)
- Summary changed from Update ImportCandidates to handle single LSM files to Update ImportCandidates and Bio-Formats to handle single LSM files
comment:2 Changed 13 years ago by bwzloranger
- Owner changed from bwzloranger to mlinkert-x
- Type changed from Task to User Story
comment:3 Changed 13 years ago by mlinkert
- Sprint set to 2011-05-05 (11)
Updating Bio-Formats to ungroup files if an .lsm is selected is quite straightforward. We already have that functionality if setGroupFiles(false) is called, so it should just be a matter of checking the file's suffix at the beginning of initFile(String) and then calling setGroupFiles(...) accordingly.
comment:4 Changed 13 years ago by Melissa Linkert <melissa@…>
(In [22f2e1d5e7e801f8bebddc53607955eda110fca2/bioformats.git]) Only group files if the .mdb file was selected.
See #3701.
comment:5 Changed 13 years ago by Melissa Linkert <melissa@…>
(In [22f2e1d5e7e801f8bebddc53607955eda110fca2/bioformats.git]) Only group files if the .mdb file was selected.
See #3701.
comment:6 Changed 13 years ago by mlinkert
- Owner changed from mlinkert-x to bwzloranger
As noted above, files will no longer be grouped if an .lsm is passed to Bio-Formats.
Re-assigning this to you Brian, in case there is anything else that needs to be done in the importer (otherwise, feel free to close).
comment:7 follow-up: ↓ 9 Changed 13 years ago by wmoore
In the Importer, just tried importing a single lsm (from within an mdb) - worked OK. Then tried importing the mdb itself..
2011-05-05 10:08:21,517 83236 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root! 2011-05-05 10:08:26,053 87772 [entQueue-0] INFO me.formats.importer.gui.FileQueueHandler - Scheduling candidate calculations(2)=[/Users/will/Documents/biology-data/Test-Import-Images/Martin/Zeiss-LSM510/sample files.mdb/sample files.mdb] 2011-05-05 10:08:26,056 87775 [entQueue-0] INFO me.formats.importer.gui.FileQueueHandler - Handling import containers(2)=[/Users/will/Documents/biology-data/Test-Import-Images/Martin/Zeiss-LSM510/sample files.mdb/sample files.mdb] 2011-05-05 10:08:30,113 91832 [2-thread-1] INFO ome.formats.importer.gui.ImportHandler - Background: Importing images 2011-05-05 10:08:30,130 91849 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - LOADING_IMAGE: sample files.mdb 2011-05-05 10:08:30,393 92112 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root! 2011-05-05 10:08:30,545 92264 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - FILE_EXCEPTION: /Users/will/Documents/biology-data/Test-Import-Images/Martin/Zeiss-LSM510/sample files.mdb/sample files.mdb 2011-05-05 10:08:30,547 92266 [2-thread-1] ERROR importer.gui.ErrorHandler$MyErrorHandler - FILE_EXCEPTION: /Users/will/Documents/biology-data/Test-Import-Images/Martin/Zeiss-LSM510/sample files.mdb/sample files.mdb 2011-05-05 10:08:30,581 92300 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root! 2011-05-05 10:08:30,589 92308 [2-thread-1] ERROR ome.formats.importer.gui.ImportHandler - Format exception while importing image.
comment:8 Changed 13 years ago by jburel
- Sprint changed from 2011-05-05 (11) to 2011-05-19 (12)
Moved from sprint 2011-05-05 (11)
comment:9 in reply to: ↑ 7 Changed 13 years ago by mlinkert
Replying to wmoore:
In the Importer, just tried importing a single lsm (from within an mdb) - worked OK. Then tried importing the mdb itself..
loci.formats.FormatException: LSM files were not found. at loci.formats.in.ZeissLSMReader.initFile(ZeissLSMReader.java:384) at loci.formats.FormatReader.setId(FormatReader.java:1072) at loci.formats.ImageReader.setId(ImageReader.java:670) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488) at loci.formats.ChannelFiller.setId(ChannelFiller.java:249) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:257) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488) at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:250) at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:499)
I'm pretty sure this was fixed in [d2cc897b4508ef46c875d459fe046e6699b4817b/bioformats.git]. Could you please try updating and see if it works?
comment:10 Changed 13 years ago by jburel
- Sprint changed from 2011-05-19 (12) to 2011-06-02 (13)
Moved from sprint 2011-05-19 (12)
comment:11 Changed 13 years ago by jburel
- Sprint changed from 2011-06-02 (13) to 2011-06-16 (14)
Moved from sprint 2011-06-02 (13)
comment:12 Changed 13 years ago by jmoore
- Owner changed from bwzloranger to wmoore
Assigning to Will for feedback.
comment:13 Changed 13 years ago by wmoore
- Resolution set to fixed
- Status changed from new to closed
This has been working for me for a while now.
Hi M,
This looks like a BF story item. Not sure if you have for this before 4.3 though.
Cheers,
B