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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

Hi M,

This looks like a BF story item. Not sure if you have for this before 4.3 though.

Cheers,

B

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: 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..

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)

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.
Last edited 13 years ago by wmoore (previous) (diff)

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.

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