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Tiff Importation Errors, BD Pathway and LiCor

PostPosted: Mon Mar 14, 2011 4:27 pm
by jzman
Hello,

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!

Re: Tiff Importation Errors, BD Pathway and LiCor

PostPosted: Mon Mar 21, 2011 10:20 pm
by mlinkert
Hi,

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.


The best thing to do is to send the full text of the error message and (if possible) the datasets that exhibit problems. This is quite easy to do from OMERO.importer; please see here for instructions:

http://openmicroscopy.org/site/support/ ... hould-i-do

Are there any known bugs with the Pathway importer?


Not at the moment. Note though that it is recommended that you select the *.exp file for import (instead of one of the TIFF files); similarly, for Li-Cor datasets it is recommended that you select the *.l2d file.

Regards,
-Melissa