Tiff Importation Errors, BD Pathway and LiCor
Posted: Mon Mar 14, 2011 4:27 pmHello,
I have a fresh 4.4.2 OMERO server installed on Windows7 that is working and everything is running fine.
However, we are having consistent problems with importing tiffs. Images from two pieces of equipment have had troubles importing: BD Pathway (tif, exp) and LiCOR (tiff).
When I try and import using a mac or windows client using the BD Pathway setting, I get the message that adding files to the queue has produced errors.
Are there any known bugs with the Pathway importer?
In the debug text, the client sees the tiff files and skips them. I have tried on multiple machines and with multiple data sets (384-well plates).
Thanks for any advice!
Jonny
PS: Here is the debug text:
And here is my diagnostics output:
I have a fresh 4.4.2 OMERO server installed on Windows7 that is working and everything is running fine.
However, we are having consistent problems with importing tiffs. Images from two pieces of equipment have had troubles importing: BD Pathway (tif, exp) and LiCOR (tiff).
When I try and import using a mac or windows client using the BD Pathway setting, I get the message that adding files to the queue has produced errors.
Are there any known bugs with the Pathway importer?
In the debug text, the client sees the tiff files and skips them. I have tried on multiple machines and with multiple data sets (384-well plates).
Thanks for any advice!
Jonny
PS: Here is the debug text:
- Code: Select all
2011-03-14 12:17:37,773 178913 [1-thread-1] DEBUG importer.gui.ErrorHandler$MyErrorHandler - UNKNOWN_FORMAT: K:\Jonny\TestDir\B-000001-1\Well A004\GFP (Re-analysis 001).adf
2011-03-14 12:17:37,944 179084 [1-thread-1] DEBUG importer.gui.ErrorHandler$MyErrorHandler - UNKNOWN_FORMAT: K:\Jonny\TestDir\B-000001-1\Well A004\GFP.adf
2011-03-14 12:17:37,991 179131 [1-thread-1] DEBUG importer.gui.ErrorHandler$MyErrorHandler - UNKNOWN_FORMAT: K:\Jonny\TestDir\B-000001-1\Well A004\Hoechst (Re-analysis 001).adf
2011-03-14 12:17:38,116 179256 [1-thread-1] DEBUG me.formats.importer.gui.FileQueueHandler - SCANNING: Depth:2 Num: 100 Tot: 105 File: ge Thumbnail.bmp
2011-03-14 12:17:38,163 179303 [1-thread-1] DEBUG importer.gui.ErrorHandler$MyErrorHandler - UNKNOWN_FORMAT: K:\Jonny\TestDir\B-000001-1\Well A004\Hoechst.adf
2011-03-14 12:17:38,194 179334 [1-thread-1] DEBUG importer.gui.ErrorHandler$MyErrorHandler - UNKNOWN_FORMAT: K:\Jonny\TestDir\B-000001-1\Well A004\No ROI.roi
2011-03-14 12:17:38,225 179365 [1-thread-1] DEBUG importer.gui.ErrorHandler$MyErrorHandler - UNKNOWN_FORMAT: K:\Jonny\TestDir\B-000001-1\Well A004\Nucleus (Re-analysis 001).roi
2011-03-14 12:17:38,256 179396 [1-thread-1] DEBUG importer.gui.ErrorHandler$MyErrorHandler - UNKNOWN_FORMAT: K:\Jonny\TestDir\B-000001-1\Well A004\Peroxisomes (Re-analysis 001).roi
2011-03-14 12:17:38,288 179428 [1-thread-1] ERROR importer.gui.ErrorHandler$MyErrorHandler - FILE_EXCEPTION: K:\Jonny\TestDir\B-000001-1\Well A004\Well A004_LaserAFData.txt
2011-03-14 12:17:38,303 179443 [1-thread-1] DEBUG me.formats.importer.gui.FileQueueHandler - SCANNING: Depth:0 Num: 105 Tot: 105 File: stDir\B-000001-1
2011-03-14 12:17:38,303 179443 [1-thread-1] INFO ome.formats.importer.ImportCandidates - 105 file(s) parsed into 39 group(s) with 105 call(s) to setId in 4479ms. (4572ms total) [62 unknowns]
2011-03-14 12:17:38,303 179443 [entQueue-0] INFO me.formats.importer.gui.FileQueueHandler - Handling import containers(2)=[K:\Jonny\TestDir\B-000001-1]
2011-03-14 12:17:38,303 179443 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Selected file filter: FormatFileFilter: BD Pathway (*.exp, *.tif)
2011-03-14 12:17:38,303 179443 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A001\GFP (Re-analysis 001) - Graph.bmp (BD Pathway != Windows Bitmap)
2011-03-14 12:17:38,303 179443 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A001\GFP - Graph.bmp (BD Pathway != Windows Bitmap)
2011-03-14 12:17:38,303 179443 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A001\GFP - n000000 - Sub Objects (Re-analysis 001).bmp (BD Pathway != Windows Bitmap)
2011-03-14 12:17:38,303 179443 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A001\GFP - n000000.tif (BD Pathway != Tagged Image File Format)
2011-03-14 12:17:38,303 179443 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A001\GFP - n000001.tif (BD Pathway != Tagged Image File Format)
2011-03-14 12:17:38,303 179443 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A001\GFP Image Thumbnail.bmp (BD Pathway != Windows Bitmap)
2011-03-14 12:17:38,303 179443 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A001\Hoechst (Re-analysis 001) - Graph.bmp (BD Pathway != Windows Bitmap)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A001\Hoechst - Graph.bmp (BD Pathway != Windows Bitmap)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A001\Hoechst - n000000.tif (BD Pathway != Tagged Image File Format)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A001\Hoechst - n000001.tif (BD Pathway != Tagged Image File Format)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A001\Hoechst Image Thumbnail.bmp (BD Pathway != Windows Bitmap)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A002\GFP (Re-analysis 001) - Graph.bmp (BD Pathway != Windows Bitmap)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A002\GFP - Graph.bmp (BD Pathway != Windows Bitmap)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A002\GFP - n000000 - Sub Objects (Re-analysis 001).bmp (BD Pathway != Windows Bitmap)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A002\GFP - n000000.tif (BD Pathway != Tagged Image File Format)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A002\GFP Image Thumbnail.bmp (BD Pathway != Windows Bitmap)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A002\Hoechst (Re-analysis 001) - Graph.bmp (BD Pathway != Windows Bitmap)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A002\Hoechst - Graph.bmp (BD Pathway != Windows Bitmap)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A002\Hoechst - n000000.tif (BD Pathway != Tagged Image File Format)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A002\Hoechst - n000001.tif (BD Pathway != Tagged Image File Format)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A002\Hoechst Image Thumbnail.bmp (BD Pathway != Windows Bitmap)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A003\GFP (Re-analysis 001) - Graph.bmp (BD Pathway != Windows Bitmap)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A003\GFP - Graph.bmp (BD Pathway != Windows Bitmap)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A003\GFP - n000000 - Sub Objects (Re-analysis 001).bmp (BD Pathway != Windows Bitmap)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A003\GFP - n000000.tif (BD Pathway != Tagged Image File Format)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A003\GFP Image Thumbnail.bmp (BD Pathway != Windows Bitmap)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A003\Hoechst (Re-analysis 001) - Graph.bmp (BD Pathway != Windows Bitmap)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A003\Hoechst - Graph.bmp (BD Pathway != Windows Bitmap)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A003\Hoechst - n000000.tif (BD Pathway != Tagged Image File Format)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A003\Hoechst Image Thumbnail.bmp (BD Pathway != Windows Bitmap)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A004\GFP (Re-analysis 001) - Graph.bmp (BD Pathway != Windows Bitmap)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A004\GFP - Graph.bmp (BD Pathway != Windows Bitmap)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A004\GFP - n000000 - Sub Objects (Re-analysis 001).bmp (BD Pathway != Windows Bitmap)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A004\GFP - n000000.tif (BD Pathway != Tagged Image File Format)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A004\GFP Image Thumbnail.bmp (BD Pathway != Windows Bitmap)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A004\Hoechst (Re-analysis 001) - Graph.bmp (BD Pathway != Windows Bitmap)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A004\Hoechst - Graph.bmp (BD Pathway != Windows Bitmap)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A004\Hoechst - n000000.tif (BD Pathway != Tagged Image File Format)
2011-03-14 12:17:38,319 179459 [entQueue-0] DEBUG me.formats.importer.gui.FileQueueHandler - Skipping K:\Jonny\TestDir\B-000001-1\Well A004\Hoechst Image Thumbnail.bmp (BD Pathway != Windows Bitmap)
2011-03-14 12:18:02,823 203963 [4-thread-1] DEBUG
And here is my diagnostics output:
- Code: Select all
PS C:\OMERO.server-Beta-4.2.2> .\bin\omero admin diagnostics
================================================================================
OMERO Diagnostics Beta4.2.2-r8718-Beta4.2-b56
================================================================================
Commands: java -version 1.6.0 (C:\Windows\system32\java.EXE)
Commands: python -V 2.5.5 (C:\Python25\python.EXE)
Commands: icegridnode --version 3.3.1 (C:\Ice-3.3.1\bin\icegridnode.EXE)
Commands: icegridadmin --version 3.3.1 (C:\Ice-3.3.1\bin\icegridadmin.EXE)
Commands: psql --version 8.3.14 (C:\Program Files (x86)\PostgreSQL\8.3\bin\psql.EXE -- 2 others)
Server: icegridnode running
Server: Blitz-0 active (pid = 2080, enabled)
Server: DropBox inactive (disabled)
Server: FileServer active (pid = 1284, enabled)
Server: Indexer-0 active (pid = 2348, enabled)
Server: MonitorServer inactive (disabled)
Server: OMERO.Glacier2 active (pid = 3092, enabled)
Server: OMERO.IceStorm active (pid = 2456, enabled)
Server: Processor-0 active (pid = 2804, enabled)
Server: Repository-1 error: node `repo' couldn't be reached:
the node is not active
Server: Tables-0 inactive (disabled)
Server: TestDropBox inactive (enabled)
Log dir: C:\OMERO.server-Beta-4.2.2\var\log exists
Log files: Blitz-0.log 11.0 MB errors=29 warnings=70
Log files: DropBox.log 1.0 KB errors=4 warnings=0
Log files: FileServer.log 0.0 KB
Log files: Indexer-0.log 555.0 KB errors=1 warnings=45
Log files: MonitorServer.log 2.0 KB errors=3 warnings=0
Log files: OMEROweb-DEBUG.log 22.0 KB
Log files: OMEROweb.log 26.0 KB errors=1 warnings=0
Log files: Processor-0.log 25.0 KB errors=0 warnings=4
Log files: Tables-0.log n/a
Log files: TestDropBox.log n/a
Log files: master.err 0.0 KB
Log files: master.out 0.0 KB
Log files: Total size 12.34 MB
Parsing Blitz-0.log:[line:76] => Server restarted <=
Parsing Blitz-0.log:[line:1492] => Server restarted <=
Parsing Blitz-0.log:[line:41308] => Server restarted <=
Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:Error printing text
PATH=%SystemRoot%\system32\WindowsPowerShell\v1.0\;C:\Python25\;C:\Program Files (x86)\Symyx\Symyx Draw 4.0\lib;C:\Windo
ws\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\; ;C:\Program Files\MySQL\MyS
QL Server 5.1\bin;C:\Ice-3.3.1\bin;C:\Program Files (x86)\PostgreSQL\8.3\bin;C:\Program Files\CellProfiler\;C:\Program F
iles (x86)\vigra\bin:C:\Ice-3.3.1\bin
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)
OMERO data dir: '/OMERO' Exists? True Is writable? True
OMERO.web status... DEVELOPMENT: You will have to check status by hand!