[ome-users] Re: Matlab PixelSlice conversion problem
Anh Vu
anh.q.vu at gmail.com
Wed Aug 24 01:31:13 BST 2005
This is the output of running the newtest chain against a data set of
12bits images.
ome execute -a 9 -d 1 -f
ome: getOMESession: found existing userState(s)
ome: createWithKey: updating userState
ome: createWithKey: returning session
Executing Analysis Chain `New Test Chain`
ome: getOMESession: found existing userState(s)
ome: createWithKey: updating userState
ome: createWithKey: returning session
ome: Loading attribute type package OME::SemanticType::__Experimenter
ome: Loading data table package OME::DataTable::__EXPERIMENTERS
ome: Loading attribute type package OME::SemanticType::__Group
ome: Loading data table package OME::DataTable::__GROUPS
ome: Round 1...
ome: isNodeReady(New Test,1)
ome: getPredecessorMEX(43)
ome: from I 34 Create pixels slices
ome: to I 32 New Test
ome: isNodeReady(New Test,2)
ome: getPredecessorMEX(43)
ome: from I 34 Create pixels slices
ome: to I 32 New Test
ome: isNodeReady(New Test,3)
ome: getPredecessorMEX(43)
ome: from I 34 Create pixels slices
ome: to I 32 New Test
ome: isNodeReady(New Test,4)
ome: getPredecessorMEX(43)
ome: from I 34 Create pixels slices
ome: to I 32 New Test
ome: isNodeReady(New Test,5)
ome: getPredecessorMEX(43)
ome: from I 34 Create pixels slices
ome: to I 32 New Test
ome: isNodeReady(New Test,7)
ome: getPredecessorMEX(43)
ome: from I 34 Create pixels slices
ome: to I 32 New Test
ome: isNodeReady(New Test,8)
ome: getPredecessorMEX(43)
ome: from I 34 Create pixels slices
ome: to I 32 New Test
ome: isNodeReady(New Test,9)
ome: getPredecessorMEX(43)
ome: from I 34 Create pixels slices
ome: to I 32 New Test
ome: isNodeReady(New Test,10)
ome: getPredecessorMEX(43)
ome: from I 34 Create pixels slices
ome: to I 32 New Test
ome: isNodeReady(New Test,6)
ome: getPredecessorMEX(43)
ome: from I 34 Create pixels slices
ome: to I 32 New Test
ome: isNodeReady(Image import,1)
ome: getPredecessorMEX(41)
ome: from G 35 Original files
ome: to I 33 Image import
1/31: [IN PROGRESS] Start Execution of Analysis Chain
ome: executeNodeWithTarget(Image import,1)
ome: getUniversalExecution(
ome: isNodeReady(Image import,2)
ome: getPredecessorMEX(41)
ome: from G 35 Original files
ome: to I 33 Image import
ome: executeNodeWithTarget(Image import,2)
ome: getUniversalExecution(
ome: isNodeReady(Image import,3)
ome: getPredecessorMEX(41)
ome: from G 35 Original files
ome: to I 33 Image import
ome: executeNodeWithTarget(Image import,3)
ome: getUniversalExecution(
ome: isNodeReady(Image import,4)
ome: getPredecessorMEX(41)
ome: from G 35 Original files
ome: to I 33 Image import
ome: executeNodeWithTarget(Image import,4)
ome: getUniversalExecution(
ome: isNodeReady(Image import,5)
ome: getPredecessorMEX(41)
ome: from G 35 Original files
ome: to I 33 Image import
ome: executeNodeWithTarget(Image import,5)
ome: getUniversalExecution(
ome: isNodeReady(Image import,7)
ome: getPredecessorMEX(41)
ome: from G 35 Original files
ome: to I 33 Image import
ome: executeNodeWithTarget(Image import,7)
ome: getUniversalExecution(
ome: isNodeReady(Image import,8)
ome: getPredecessorMEX(41)
ome: from G 35 Original files
ome: to I 33 Image import
ome: executeNodeWithTarget(Image import,8)
ome: getUniversalExecution(
ome: isNodeReady(Image import,9)
ome: getPredecessorMEX(41)
ome: from G 35 Original files
ome: to I 33 Image import
ome: executeNodeWithTarget(Image import,9)
ome: getUniversalExecution(
ome: isNodeReady(Image import,10)
ome: getPredecessorMEX(41)
ome: from G 35 Original files
ome: to I 33 Image import
ome: executeNodeWithTarget(Image import,10)
ome: getUniversalExecution(
ome: isNodeReady(Image import,6)
ome: getPredecessorMEX(41)
ome: from G 35 Original files
ome: to I 33 Image import
ome: executeNodeWithTarget(Image import,6)
ome: getUniversalExecution(
ome: isNodeReady(Create pixels slices,1)
ome: getPredecessorMEX(42)
ome: from I 33 Image import
ome: to I 34 Create pixels slices
ome: executeNodeWithTarget(Create pixels slices,1)
ome: getUniversalExecution(
ome: getPredecessorMEX(42)
ome: from I 33 Image import
ome: to I 34 Create pixels slices
ome: Loading attribute type package OME::SemanticType::__Pixels
ome: Loading data table package OME::DataTable::__IMAGE_PIXELS
ome: Loading attribute type package OME::SemanticType::__Repository
ome: Loading data table package OME::DataTable::__REPOSITORIES
ome: Executing!
ome: Loading attribute type package OME::SemanticType::__PixelsSlice
ome: Loading data table package OME::DataTable::__PIXELS_SLICE
ome: isNodeReady(Create pixels slices,2)
ome: getPredecessorMEX(42)
ome: from I 33 Image import
ome: to I 34 Create pixels slices
ome: executeNodeWithTarget(Create pixels slices,2)
ome: getUniversalExecution(
ome: getPredecessorMEX(42)
ome: from I 33 Image import
ome: to I 34 Create pixels slices
ome: Executing!
ome: isNodeReady(Create pixels slices,3)
ome: getPredecessorMEX(42)
ome: from I 33 Image import
ome: to I 34 Create pixels slices
ome: executeNodeWithTarget(Create pixels slices,3)
ome: getUniversalExecution(
ome: getPredecessorMEX(42)
ome: from I 33 Image import
ome: to I 34 Create pixels slices
ome: Executing!
ome: isNodeReady(Create pixels slices,4)
ome: getPredecessorMEX(42)
ome: from I 33 Image import
ome: to I 34 Create pixels slices
ome: executeNodeWithTarget(Create pixels slices,4)
ome: getUniversalExecution(
ome: getPredecessorMEX(42)
ome: from I 33 Image import
ome: to I 34 Create pixels slices
ome: Executing!
ome: isNodeReady(Create pixels slices,5)
ome: getPredecessorMEX(42)
ome: from I 33 Image import
ome: to I 34 Create pixels slices
ome: executeNodeWithTarget(Create pixels slices,5)
ome: getUniversalExecution(
ome: getPredecessorMEX(42)
ome: from I 33 Image import
ome: to I 34 Create pixels slices
ome: Executing!
ome: isNodeReady(Create pixels slices,7)
ome: getPredecessorMEX(42)
ome: from I 33 Image import
ome: to I 34 Create pixels slices
ome: executeNodeWithTarget(Create pixels slices,7)
ome: getUniversalExecution(
ome: getPredecessorMEX(42)
ome: from I 33 Image import
ome: to I 34 Create pixels slices
ome: Executing!
ome: isNodeReady(Create pixels slices,8)
ome: getPredecessorMEX(42)
ome: from I 33 Image import
ome: to I 34 Create pixels slices
ome: executeNodeWithTarget(Create pixels slices,8)
ome: getUniversalExecution(
ome: getPredecessorMEX(42)
ome: from I 33 Image import
ome: to I 34 Create pixels slices
ome: Executing!
ome: isNodeReady(Create pixels slices,9)
ome: getPredecessorMEX(42)
ome: from I 33 Image import
ome: to I 34 Create pixels slices
ome: executeNodeWithTarget(Create pixels slices,9)
ome: getUniversalExecution(
ome: getPredecessorMEX(42)
ome: from I 33 Image import
ome: to I 34 Create pixels slices
ome: Executing!
ome: isNodeReady(Create pixels slices,10)
ome: getPredecessorMEX(42)
ome: from I 33 Image import
ome: to I 34 Create pixels slices
ome: executeNodeWithTarget(Create pixels slices,10)
ome: getUniversalExecution(
ome: getPredecessorMEX(42)
ome: from I 33 Image import
ome: to I 34 Create pixels slices
ome: Executing!
ome: isNodeReady(Create pixels slices,6)
ome: getPredecessorMEX(42)
ome: from I 33 Image import
ome: to I 34 Create pixels slices
ome: executeNodeWithTarget(Create pixels slices,6)
ome: getUniversalExecution(
ome: getPredecessorMEX(42)
ome: from I 33 Image import
ome: to I 34 Create pixels slices
ome: Executing!
ome: isNodeReady(Original files,0)
ome: executeNodeWithTarget(Original files,0)
ome: getUniversalExecution(
ome: Round 2...
ome: isNodeReady(New Test,1)
ome: getPredecessorMEX(43)
ome: from I 34 Create pixels slices
ome: to I 32 New Test
ome: executeNodeWithTarget(New Test,1)
ome: getUniversalExecution(
ome: getPredecessorMEX(43)
ome: from I 34 Create pixels slices
ome: to I 32 New Test
ome: Executing!
ome: Matlab src dir is /home/avu/OME/src/matlab
ome: Matlab exec is /usr/local/matlab/bin/matlab
22/31: [IN PROGRESS] Executing `New Test`
X connection to localhost:10.0 broken (explicit kill or server shutdown).
DIMS are 0,0,0,0,0,671,511,0,0,0
ome_input_0_PixelsArray =
getROI(openConnectionOMEIS('http://batch2112b.ucr.edu/cgi-bin/omeis'),265,0,0,0,0,0,671,511,0,0,0);
outbuffer is
outbuffer is
dims are sizeX=672, sizeY=512, sizeZ=1, sizeC=1, sizeT=1
ome: ***** Command to Matlab: ome_output_0_PixelsArray =
newtest(ome_input_0_PixelsArray);
ome: Loading attribute type package OME::SemanticType::__DisplayOptions
ome: Loading data table package OME::DataTable::__DISPLAY_OPTIONS
ome: Loading attribute type package OME::SemanticType::__DisplayChannel
ome: Loading data table package OME::DataTable::__DISPLAY_CHANNELS
ome: Loading attribute type package OME::SemanticType::__PixelChannelComponent
ome: Loading data table package OME::DataTable::__CHANNEL_COMPONENTS
ome: Loading attribute type package OME::SemanticType::__LogicalChannel
ome: Loading data table package OME::DataTable::__LOGICAL_CHANNELS
ome: Loading attribute type package OME::SemanticType::__LightSource
ome: Loading data table package OME::DataTable::__LIGHT_SOURCES
ome: Loading attribute type package OME::SemanticType::__Instrument
ome: Loading data table package OME::DataTable::__INSTRUMENTS
ome: Loading attribute type package OME::SemanticType::__Detector
ome: Loading data table package OME::DataTable::__DETECTORS
ome: Loading attribute type package OME::SemanticType::__OTF
ome: Loading data table package OME::DataTable::__OTFS
ome: Loading attribute type package OME::SemanticType::__Filter
ome: Loading data table package OME::DataTable::__FILTER
ome: Loading attribute type package OME::SemanticType::__Objective
ome: Loading data table package OME::DataTable::__OBJECTIVES
ome: isNodeReady(New Test,2)
ome: getPredecessorMEX(43)
ome: from I 34 Create pixels slices
ome: to I 32 New Test
ome: executeNodeWithTarget(New Test,2)
ome: getUniversalExecution(
ome: getPredecessorMEX(43)
ome: from I 34 Create pixels slices
ome: to I 32 New Test
ome: Executing!
ome: Matlab src dir is /home/avu/OME/src/matlab
ome: Matlab exec is /usr/local/matlab/bin/matlab
23/31: [IN PROGRESS] Executing `New Test`
X connection to localhost:10.0 broken (explicit kill or server shutdown).
DIMS are 0,0,0,0,0,671,511,0,0,0
ome_input_0_PixelsArray =
getROI(openConnectionOMEIS('http://batch2112b.ucr.edu/cgi-bin/omeis'),266,0,0,0,0,0,671,511,0,0,0);
outbuffer is
outbuffer is
dims are sizeX=672, sizeY=512, sizeZ=1, sizeC=1, sizeT=1
ome: ***** Command to Matlab: ome_output_0_PixelsArray =
newtest(ome_input_0_PixelsArray);
ome: isNodeReady(New Test,3)
ome: getPredecessorMEX(43)
ome: from I 34 Create pixels slices
ome: to I 32 New Test
ome: executeNodeWithTarget(New Test,3)
ome: getUniversalExecution(
ome: getPredecessorMEX(43)
ome: from I 34 Create pixels slices
ome: to I 32 New Test
ome: Executing!
ome: Matlab src dir is /home/avu/OME/src/matlab
ome: Matlab exec is /usr/local/matlab/bin/matlab
X connection to localhost:10.0 broken (explicit kill or server shutdown).
24/31: [IN PROGRESS] Executing `New Test`
DIMS are 0,0,0,0,0,671,511,0,0,0
ome_input_0_PixelsArray =
getROI(openConnectionOMEIS('http://batch2112b.ucr.edu/cgi-bin/omeis'),267,0,0,0,0,0,671,511,0,0,0);
outbuffer is
outbuffer is
dims are sizeX=672, sizeY=512, sizeZ=1, sizeC=1, sizeT=1
ome: ***** Command to Matlab: ome_output_0_PixelsArray =
newtest(ome_input_0_PixelsArray);
ome: isNodeReady(New Test,4)
ome: getPredecessorMEX(43)
ome: from I 34 Create pixels slices
ome: to I 32 New Test
ome: executeNodeWithTarget(New Test,4)
ome: getUniversalExecution(
ome: getPredecessorMEX(43)
ome: from I 34 Create pixels slices
ome: to I 32 New Test
ome: Executing!
ome: Matlab src dir is /home/avu/OME/src/matlab
ome: Matlab exec is /usr/local/matlab/bin/matlab
25/31: [IN PROGRESS] Executing `New Test`
X connection to localhost:10.0 broken (explicit kill or server shutdown).
DIMS are 0,0,0,0,0,671,511,0,0,0
ome_input_0_PixelsArray =
getROI(openConnectionOMEIS('http://batch2112b.ucr.edu/cgi-bin/omeis'),268,0,0,0,0,0,671,511,0,0,0);
outbuffer is
outbuffer is
dims are sizeX=672, sizeY=512, sizeZ=1, sizeC=1, sizeT=1
ome: ***** Command to Matlab: ome_output_0_PixelsArray =
newtest(ome_input_0_PixelsArray);
ome: isNodeReady(New Test,5)
ome: getPredecessorMEX(43)
ome: from I 34 Create pixels slices
ome: to I 32 New Test
ome: executeNodeWithTarget(New Test,5)
ome: getUniversalExecution(
ome: getPredecessorMEX(43)
ome: from I 34 Create pixels slices
ome: to I 32 New Test
ome: Executing!
ome: Matlab src dir is /home/avu/OME/src/matlab
ome: Matlab exec is /usr/local/matlab/bin/matlab
X connection to localhost:10.0 broken (explicit kill or server shutdown).
26/31: [IN PROGRESS] Executing `New Test`
DIMS are 0,0,0,0,0,671,511,0,0,0
ome_input_0_PixelsArray =
getROI(openConnectionOMEIS('http://batch2112b.ucr.edu/cgi-bin/omeis'),269,0,0,0,0,0,671,511,0,0,0);
outbuffer is
outbuffer is
dims are sizeX=672, sizeY=512, sizeZ=1, sizeC=1, sizeT=1
ome: ***** Command to Matlab: ome_output_0_PixelsArray =
newtest(ome_input_0_PixelsArray);
ome: isNodeReady(New Test,7)
ome: getPredecessorMEX(43)
ome: from I 34 Create pixels slices
ome: to I 32 New Test
ome: executeNodeWithTarget(New Test,7)
ome: getUniversalExecution(
ome: getPredecessorMEX(43)
ome: from I 34 Create pixels slices
ome: to I 32 New Test
ome: Executing!
ome: Matlab src dir is /home/avu/OME/src/matlab
ome: Matlab exec is /usr/local/matlab/bin/matlab
27/31: [IN PROGRESS] Executing `New Test`
X connection to localhost:10.0 broken (explicit kill or server shutdown).
DIMS are 0,0,0,0,0,671,511,0,0,0
ome_input_0_PixelsArray =
getROI(openConnectionOMEIS('http://batch2112b.ucr.edu/cgi-bin/omeis'),271,0,0,0,0,0,671,511,0,0,0);
outbuffer is
outbuffer is
dims are sizeX=672, sizeY=512, sizeZ=1, sizeC=1, sizeT=1
ome: ***** Command to Matlab: ome_output_0_PixelsArray =
newtest(ome_input_0_PixelsArray);
ome: isNodeReady(New Test,8)
ome: getPredecessorMEX(43)
ome: from I 34 Create pixels slices
ome: to I 32 New Test
ome: executeNodeWithTarget(New Test,8)
ome: getUniversalExecution(
ome: getPredecessorMEX(43)
ome: from I 34 Create pixels slices
ome: to I 32 New Test
ome: Executing!
ome: Matlab src dir is /home/avu/OME/src/matlab
ome: Matlab exec is /usr/local/matlab/bin/matlab
X connection to localhost:10.0 broken (explicit kill or server shutdown).
28/31: [IN PROGRESS] Executing `New Test`
DIMS are 0,0,0,0,0,671,511,0,0,0
ome_input_0_PixelsArray =
getROI(openConnectionOMEIS('http://batch2112b.ucr.edu/cgi-bin/omeis'),272,0,0,0,0,0,671,511,0,0,0);
outbuffer is
outbuffer is
dims are sizeX=672, sizeY=512, sizeZ=1, sizeC=1, sizeT=1
ome: ***** Command to Matlab: ome_output_0_PixelsArray =
newtest(ome_input_0_PixelsArray);
ome: isNodeReady(New Test,9)
ome: getPredecessorMEX(43)
ome: from I 34 Create pixels slices
ome: to I 32 New Test
ome: executeNodeWithTarget(New Test,9)
ome: getUniversalExecution(
ome: getPredecessorMEX(43)
ome: from I 34 Create pixels slices
ome: to I 32 New Test
ome: Executing!
ome: Matlab src dir is /home/avu/OME/src/matlab
ome: Matlab exec is /usr/local/matlab/bin/matlab
29/31: [IN PROGRESS] Executing `New Test`
X connection to localhost:10.0 broken (explicit kill or server shutdown).
DIMS are 0,0,0,0,0,671,511,0,0,0
ome_input_0_PixelsArray =
getROI(openConnectionOMEIS('http://batch2112b.ucr.edu/cgi-bin/omeis'),273,0,0,0,0,0,671,511,0,0,0);
outbuffer is
outbuffer is
dims are sizeX=672, sizeY=512, sizeZ=1, sizeC=1, sizeT=1
ome: ***** Command to Matlab: ome_output_0_PixelsArray =
newtest(ome_input_0_PixelsArray);
ome: isNodeReady(New Test,10)
ome: getPredecessorMEX(43)
ome: from I 34 Create pixels slices
ome: to I 32 New Test
ome: executeNodeWithTarget(New Test,10)
ome: getUniversalExecution(
ome: getPredecessorMEX(43)
ome: from I 34 Create pixels slices
ome: to I 32 New Test
ome: Executing!
ome: Matlab src dir is /home/avu/OME/src/matlab
ome: Matlab exec is /usr/local/matlab/bin/matlab
X connection to localhost:10.0 broken (explicit kill or server shutdown).
30/31: [IN PROGRESS] Executing `New Test`
DIMS are 0,0,0,0,0,671,511,0,0,0
ome_input_0_PixelsArray =
getROI(openConnectionOMEIS('http://batch2112b.ucr.edu/cgi-bin/omeis'),274,0,0,0,0,0,671,511,0,0,0);
outbuffer is
outbuffer is
dims are sizeX=672, sizeY=512, sizeZ=1, sizeC=1, sizeT=1
ome: ***** Command to Matlab: ome_output_0_PixelsArray =
newtest(ome_input_0_PixelsArray);
ome: isNodeReady(New Test,6)
ome: getPredecessorMEX(43)
ome: from I 34 Create pixels slices
ome: to I 32 New Test
ome: executeNodeWithTarget(New Test,6)
ome: getUniversalExecution(
ome: getPredecessorMEX(43)
ome: from I 34 Create pixels slices
ome: to I 32 New Test
ome: Executing!
ome: Matlab src dir is /home/avu/OME/src/matlab
ome: Matlab exec is /usr/local/matlab/bin/matlab
31/31: [IN PROGRESS] Executing `New Test`
X connection to localhost:10.0 broken (explicit kill or server shutdown).
DIMS are 0,0,0,0,0,671,511,0,0,0
ome_input_0_PixelsArray =
getROI(openConnectionOMEIS('http://batch2112b.ucr.edu/cgi-bin/omeis'),270,0,0,0,0,0,671,511,0,0,0);
outbuffer is
outbuffer is
dims are sizeX=672, sizeY=512, sizeZ=1, sizeC=1, sizeT=1
ome: ***** Command to Matlab: ome_output_0_PixelsArray =
newtest(ome_input_0_PixelsArray);
ome: Round 3...
Exiting...
[avu at batch2112b Tests]$ 31/31: [FINISHED]
Exiting...
I've also included screenshots of the newtest results for two of the
images in a dataset of 12bits image.
-Anh
On 8/22/05, Tom Macura <macurato at grc.nia.nih.gov> wrote:
> Hi,
>
> Thanks for sending the XML files. On my laptop (OS 10.3) I tried
> importing 70 tiffs: some 12bit, some 8bit, some RGB colour. When I ran
> your chain against all these images the chain executed correctly.
>
> You might having encountered a bug, e.g. a memory leak, that is system
> dependent. . Our Linux servers are busy with heavy computing for
> probably the whole week.
>
> Perhaps you can try to use this MatlabHandler.pm (it just has
> additional debug information) for the time being. It belongs under
> OME/Analysis/Handlers in your system Perl directory. (Or copy it into
> your OME distribution and reinstall).
>
> Please send me the full output from the command-line if you encounter
> problems again.
>
> Sorry you are having trouble. If you wait, probably 2 weeks, we will be
> using the Matlab Handler to compute about 50 Matlab modules against
> 5000 images. I am sure that after this "stress test" many such bugs
> will be isolated and fixed. I hope so anyway.
>
> Tom
>
>
>
> On Aug 19, 2005, at 5:40 PM, Anh Vu wrote:
>
> > Here are the three files I have for the execution chain NewTest, which
> > is the same as the matlabtest.m file I had earlier.
>
>
>
>
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