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TIFF: adjust optimal tile height if tiles have height of 1 #1009

Merged
merged 1 commit into from
Mar 31, 2014
Merged

TIFF: adjust optimal tile height if tiles have height of 1 #1009

merged 1 commit into from
Mar 31, 2014

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melissalinkert
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This prevents callers that rely on the optimal tile height from reading
one row at a time from small images. If the images are sufficiently
wide that only 1 row of pixels will fit in memory, then the optimal
height will still be 1.

Fixes http://trac.openmicroscopy.org.uk/ome/ticket/11850

@melissalinkert
TIFF: adjust optimal tile height if tiles have height 1
2aea1c3 
This prevents callers that rely on the optimal tile height from reading
one row at a time from small images.  If the images are sufficiently
wide that only 1 row of pixels will fit in memory, then the optimal
height will still be 1.

Fixes #11850.
@will-moore
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The 2 sample files from QA were imported in 13 secs and 15 secs via CLI. Much improved speed.

Good to merge.

Created session 03cb6c22-a21b-4455-98bd-1949cbd03831 (will@localhost:4064). Idle timeout: 10.0 min. Current group: read-ann
2014-03-31 11:48:50,335 278        [      main] INFO          ome.formats.importer.ImportConfig - OMERO Version: 5.0.0-DEV-ice35
2014-03-31 11:48:50,375 318        [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 5.0.0-DEV-ice35 revision: d760635 date: 31 March 2014
2014-03-31 11:48:50,390 333        [      main] INFO   formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2014-03-31 11:48:50,874 817        [      main] INFO      ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM
2014-03-31 11:48:54,852 4795       [      main] INFO      ome.formats.importer.ImportCandidates - 2 file(s) parsed into 2 group(s) with 2 call(s) to setId in 3974ms. (3979ms total) [0 unknowns]
2014-03-31 11:48:55,277 5220       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:4064
2014-03-31 11:48:56,391 6334       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back
2014-03-31 11:48:57,346 7289       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Server: 5.0.0
2014-03-31 11:48:57,347 7290       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Client: 5.0.0-DEV-ice35
2014-03-31 11:48:57,347 7290       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Java Version: 1.6.0_65
2014-03-31 11:48:57,347 7290       [      main] INFO       ome.formats.OMEROMetadataStoreClient - OS Name: Mac OS X
2014-03-31 11:48:57,347 7290       [      main] INFO       ome.formats.OMEROMetadataStoreClient - OS Arch: x86_64
2014-03-31 11:48:57,347 7290       [      main] INFO       ome.formats.OMEROMetadataStoreClient - OS Version: 10.8.5
2014-03-31 11:48:57,781 7724       [      main] INFO   ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION
2014-03-31 11:48:57,885 7828       [      main] INFO          ome.formats.importer.ImportConfig - OMERO Version: 5.0.0-DEV-ice35
2014-03-31 11:48:57,886 7829       [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 5.0.0-DEV-ice35 revision: d760635 date: 31 March 2014
2014-03-31 11:48:58,608 8551       [      main] INFO   ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START
2014-03-31 11:48:58,664 8607       [      main] INFO   ts.importer.transfers.UploadFileTransfer - Transferring /Users/wmoore/Documents/biology-data/from_QA_apache_repo/7942/C-4-XY_00029.OME.tiff...
2014-03-31 11:48:58,709 8652       [      main] INFO   ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /Users/wmoore/Documents/biology-data/from_QA_apache_repo/7942/C-4-XY_00029.OME.tiff
2014-03-31 11:48:58,919 8862       [      main] INFO   ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /Users/wmoore/Documents/biology-data/from_QA_apache_repo/7942/C-4-XY_00029.OME.tiff
2014-03-31 11:48:59,151 9094       [      main] INFO   ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END
2014-03-31 11:49:01,006 10949      [l.Client-0] INFO   ormats.importer.cli.LoggingImportMonitor - METADATA_IMPORTED Step: 1 of 5  Logfile: 24
2014-03-31 11:49:01,552 11495      [l.Client-1] INFO   ormats.importer.cli.LoggingImportMonitor - PIXELDATA_PROCESSED Step: 2 of 5  Logfile: 24
2014-03-31 11:49:03,276 13219      [l.Client-0] INFO   ormats.importer.cli.LoggingImportMonitor - THUMBNAILS_GENERATED Step: 3 of 5  Logfile: 24
2014-03-31 11:49:03,315 13258      [l.Client-1] INFO   ormats.importer.cli.LoggingImportMonitor - METADATA_PROCESSED Step: 4 of 5  Logfile: 24
2014-03-31 11:49:03,343 13286      [l.Client-0] INFO   ormats.importer.cli.LoggingImportMonitor - OBJECTS_RETURNED Step: 5 of 5  Logfile: 24
2014-03-31 11:49:03,733 13676      [l.Client-1] INFO   ormats.importer.cli.LoggingImportMonitor - IMPORT_DONE Imported file: /Users/wmoore/Documents/biology-data/from_QA_apache_repo/7942/C-4-XY_00029.OME.tiff
Imported pixels:
1
Other imported objects:
Fileset:1
Image:1
2014-03-31 11:49:03,734 13677      [l.Client-1] INFO      ome.formats.importer.cli.ErrorHandler - Number of errors: 0
2014-03-31 11:49:03,737 13680      [      main] INFO   ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION
2014-03-31 11:49:03,746 13689      [      main] INFO          ome.formats.importer.ImportConfig - OMERO Version: 5.0.0-DEV-ice35
2014-03-31 11:49:03,746 13689      [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 5.0.0-DEV-ice35 revision: d760635 date: 31 March 2014
2014-03-31 11:49:03,955 13898      [      main] INFO   ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START
2014-03-31 11:49:03,957 13900      [      main] INFO   ts.importer.transfers.UploadFileTransfer - Transferring /Users/wmoore/Documents/biology-data/from_QA_apache_repo/7942/fluor.OME.tiff...
2014-03-31 11:49:03,976 13919      [      main] INFO   ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /Users/wmoore/Documents/biology-data/from_QA_apache_repo/7942/fluor.OME.tiff
2014-03-31 11:49:09,034 18977      [      main] INFO   ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /Users/wmoore/Documents/biology-data/from_QA_apache_repo/7942/fluor.OME.tiff
2014-03-31 11:49:09,948 19891      [      main] INFO   ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END
2014-03-31 11:49:11,203 21146      [l.Client-0] INFO   ormats.importer.cli.LoggingImportMonitor - METADATA_IMPORTED Step: 1 of 5  Logfile: 27
2014-03-31 11:49:14,736 24679      [l.Client-2] INFO   ormats.importer.cli.LoggingImportMonitor - PIXELDATA_PROCESSED Step: 2 of 5  Logfile: 27
2014-03-31 11:49:17,993 27936      [l.Client-1] INFO   ormats.importer.cli.LoggingImportMonitor - THUMBNAILS_GENERATED Step: 3 of 5  Logfile: 27
2014-03-31 11:49:18,017 27960      [l.Client-0] INFO   ormats.importer.cli.LoggingImportMonitor - METADATA_PROCESSED Step: 4 of 5  Logfile: 27
2014-03-31 11:49:18,039 27982      [l.Client-2] INFO   ormats.importer.cli.LoggingImportMonitor - OBJECTS_RETURNED Step: 5 of 5  Logfile: 27
2014-03-31 11:49:18,129 28072      [l.Client-1] INFO   ormats.importer.cli.LoggingImportMonitor - IMPORT_DONE Imported file: /Users/wmoore/Documents/biology-data/from_QA_apache_repo/7942/fluor.OME.tiff
Imported pixels:
2
Other imported objects:
Fileset:2
Image:2

melissalinkert added a commit that referenced this pull request Mar 31, 2014
@melissalinkert
Merge pull request #1009 from melissalinkert/11850
a72e18c 
TIFF: adjust optimal tile height if tiles have height of 1
@melissalinkert melissalinkert merged commit a72e18c into ome:dev_5_0 Mar 31, 2014
@melissalinkert melissalinkert mentioned this pull request Apr 7, 2014
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@melissalinkert
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--rebased-to #1029

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@melissalinkert @will-moore