[ome-devel] OME-Tiff writing using LOCI calls from MATLAB, and ModuloAlongT annotation
Munro, Ian
i.munro at imperial.ac.uk
Wed Oct 29 14:26:13 GMT 2014
Hi All
I’m just in the process of checking this to ensure that the data that is read back is the same both with and without this modification.
If I run the command line 'showinf tool 'on the smaller files produced with the suggested ifd mod then I get the following in the output:
Reading pixel data (0-2)
Reading IFDs
Populating metadata
Error untangling IFDs; the OME-TIFF file may be malformed.
Error untangling IFDs; the OME-TIFF file may be malformed.
Read 3/3 planes (100%)
[done]
Is anyone else seeing this. I may have implemented the ifd mod incorrectly?
Regards
Ian
On 29 Oct 2014, at 12:44, Alexandrov, Yuriy <y.alexandrov at imperial.ac.uk<mailto:y.alexandrov at imperial.ac.uk>> wrote:
Hi All,
I checked how Sebastien’s method works on my (Win 7) machine – for my example 5 frame OPT data, it provides slightly smaller files (18M vs 20M) and works a bit faster (0.22 vs 0.34 s/frame). Frame is 1191x2559 uint16.
Initialized and used exactly as Sebastien suggests -
ifd = loci.formats.tiff.IFD();
ifd.putIFDValue(ifd.ROWS_PER_STRIP,sizeY);
%% inside loop by “index”
…
writer.getWriter(ometiffilename).saveBytes(index-1, getBytes(I), ifd);
…
So I switched to this method.
Best,
Y.
From: ome-devel [mailto:ome-devel-bounces at lists.openmicroscopy.org.uk] On Behalf Of Yellen, Gary
Sent: 28 October 2014 19:33
To: Besson, Sebastien (forwarding)
Cc: OME-devel OME
Subject: Re: [ome-devel] OME-Tiff writing using LOCI calls from MATLAB, and ModuloAlongT annotation
Hi Sebastien - Strange!
I just re-ran it:
First writing data with the hybrid Bio-Formats / Tiff() code...
Elapsed time is 1.324383 seconds.
Now writing data with all Bio-Formats code...
Elapsed time is 5.011741 seconds.
java.lang.Runtime.getRuntime.maxMemory = 492175360
Windows 7 SP1 x64
Intel Core i7-4770 (3.40GHz)
MATLAB R2014a (64-bit)
I am getting a smaller filesize now with the Bio-Formats code: 1.57MB (might have had writer.close errors before that resulted in appending), but it still take 4.7 to 5 seconds.
I wonder if it’s something related to the filesystem and file allocation/growth. My disk is only ~25% full, so shouldn’t be a big issue. I did just try both tests to an empty scratch directory; both were faster but I still see the difference (1.20 vs. 4.38 sec).
Also – the bioformats_package.jar is at the end of my static java path, right after all the MATLAB .jars. (see below at the bottom of the email.) Could this be the issue?
gary
From: Sebastien Besson [mailto:s.besson at dundee.ac.uk]
Sent: Tuesday, October 28, 2014 3:16 PM
To: Yellen, Gary
Cc: OME-devel OME
Subject: Re: [ome-devel] OME-Tiff writing using LOCI calls from MATLAB, and ModuloAlongT annotation
HI Gary,
thanks for the heads up. Strangely, with the code you attached to your email which matches my
suggested changes, I have the following result:
>> gyTestScript
First writing data with the hybrid Bio-Formats / Tiff() code...
Elapsed time is 2.321489 seconds.
Now writing data with all Bio-Formats code...
Elapsed time is 2.448038 seconds.
and both generated OME TIFFs are about 1.5-1.6MB.
Which version of MATLAB and which OS/architecture are you using?
Best,
Sebastien
On 28 Oct 2014, at 17:27, Yellen, Gary <gary_yellen at hms.harvard.edu<mailto:gary_yellen at hms.harvard.edu>> wrote:
Thanks, Sebastien.
I found that this made some improvement: The time is now 4.66 sec (vs. previous 70 sec and alternate 1.26 sec), and the filesize is slightly improved (4.5 MB, vs previous 5.3 MB and alternate 1.65 MB).
I’ve enclosed the modified code, which includes my interpretation of your suggested changes (I created the new IFD only once, and then set owriter=writer.getWriter(fname)). Please let me know if this is not quite what you meant.
Best,
Gary
From: Sebastien Besson [mailto:s.besson at dundee.ac.uk]
Sent: Tuesday, October 28, 2014 12:25 PM
To: Yellen, Gary
Cc: OME-devel OME
Subject: Re: [ome-devel] OME-Tiff writing using LOCI calls from MATLAB, and ModuloAlongT annotation
Hi Gary,
thanks for sending the code and some test data. After some debugging and with Melissa's input,
the major difference between the whole Bio-Formats version and thelibTiff version is the following
option:
tagstruct.RowsPerStrip = szY;
If writing using Bio-Formats, a workaround is to construct a loci.formats.tiff.IFD object with the
RowsPerStrip equal to the desired value, i.e.
ifd = loci.formats.tiff.IFD();
ifd.putIFDValue(ifd.ROWS_PER_STRIP, szY);
This object can then be passed to TiffWriter.saveBytes():
1- either if you initialize an ImageWriter() using
writer.getWriter(fname).saveBytes(index, getBytes(plane(:)), ifd);
2- or if you directly initialize an OMETiffWriter() using
writer.saveBytes(index, getBytes(plane(:)), ifd);
Locally adding this option brought your Bio-Formats code to similar levels of performance
in terms of file size and writing time.
Could you try this and let us know?
Sebastien
STATIC JAVA PATH
C:\Program Files\MATLAB\R2014a\java\patch
C:\Program Files\MATLAB\R2014a\java\jarext\AnimatedTransitions.jar
C:\Program Files\MATLAB\R2014a\java\jarext\ant.jar
C:\Program Files\MATLAB\R2014a\java\jarext\ant-launcher.jar
C:\Program Files\MATLAB\R2014a\java\jarext\antlr.jar
C:\Program Files\MATLAB\R2014a\java\jarext\felix.jar
C:\Program Files\MATLAB\R2014a\java\jarext\scr.jar
C:\Program Files\MATLAB\R2014a\java\jarext\axis2\activation.jar
C:\Program Files\MATLAB\R2014a\java\jarext\axis2\axiom-api.jar
C:\Program Files\MATLAB\R2014a\java\jarext\axis2\axiom-impl.jar
C:\Program Files\MATLAB\R2014a\java\jarext\axis2\axis2-adb.jar
C:\Program Files\MATLAB\R2014a\java\jarext\axis2\axis2-kernel.jar
C:\Program Files\MATLAB\R2014a\java\jarext\axis2\axis2-transport-http.jar
C:\Program Files\MATLAB\R2014a\java\jarext\axis2\axis2-transport-local.jar
C:\Program Files\MATLAB\R2014a\java\jarext\axis2\commons-httpclient.jar
C:\Program Files\MATLAB\R2014a\java\jarext\axis2\geronimo-stax-api.jar
C:\Program Files\MATLAB\R2014a\java\jarext\axis2\httpcore.jar
C:\Program Files\MATLAB\R2014a\java\jarext\axis2\mail.jar
C:\Program Files\MATLAB\R2014a\java\jarext\axis2\neethi.jar
C:\Program Files\MATLAB\R2014a\java\jarext\axis2\wsdl4j.jar
C:\Program Files\MATLAB\R2014a\java\jarext\axis2\wstx-asl.jar
C:\Program Files\MATLAB\R2014a\java\jarext\axis2\XmlSchema.jar
C:\Program Files\MATLAB\R2014a\java\jarext\batik-anim.jar
C:\Program Files\MATLAB\R2014a\java\jarext\batik-extension.jar
C:\Program Files\MATLAB\R2014a\java\jarext\batik-dom.jar
C:\Program Files\MATLAB\R2014a\java\jarext\batik-transcoder.jar
C:\Program Files\MATLAB\R2014a\java\jarext\batik-awt-util.jar
C:\Program Files\MATLAB\R2014a\java\jarext\batik-bridge.jar
C:\Program Files\MATLAB\R2014a\java\jarext\batik-gvt.jar
C:\Program Files\MATLAB\R2014a\java\jarext\batik-css.jar
C:\Program Files\MATLAB\R2014a\java\jarext\batik-parser.jar
C:\Program Files\MATLAB\R2014a\java\jarext\batik-ext.jar
C:\Program Files\MATLAB\R2014a\java\jarext\batik-gui-util.jar
C:\Program Files\MATLAB\R2014a\java\jarext\batik-svggen.jar
C:\Program Files\MATLAB\R2014a\java\jarext\batik-codec.jar
C:\Program Files\MATLAB\R2014a\java\jarext\batik-svg-dom.jar
C:\Program Files\MATLAB\R2014a\java\jarext\batik-script.jar
C:\Program Files\MATLAB\R2014a\java\jarext\batik-util.jar
C:\Program Files\MATLAB\R2014a\java\jarext\batik-swing.jar
C:\Program Files\MATLAB\R2014a\java\jarext\batik-xml.jar
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C:\Program Files\MATLAB\R2014a\java\jarext\commons-codec.jar
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C:\Program Files\MATLAB\R2014a\java\jar\ja_JP\shared_rptgen_res.jar
C:\Program Files\MATLAB\R2014a\java\jar\ja_JP\stats_res.jar
C:\Program Files\MATLAB\R2014a\java\jar\ja_JP\student_activation_res.jar
C:\Program Files\MATLAB\R2014a\java\jar\ja_JP\symbolic_editor_support_res.jar
C:\Program Files\MATLAB\R2014a\java\jar\ja_JP\timeseries_res.jar
C:\Program Files\MATLAB\R2014a\java\jar\ja_JP\webintegration_res.jar
C:\Program Files\MATLAB\R2014a\java\jar\ja_JP\web_connectivity_res.jar
C:\Program Files\MATLAB\R2014a\java\jar\ko_KR\activation_res.jar
C:\Program Files\MATLAB\R2014a\java\jar\ko_KR\install_api_res.jar
C:\Program Files\MATLAB\R2014a\java\jar\ko_KR\professional_activation_res.jar
C:\Program Files\MATLAB\R2014a\java\jar\ko_KR\shared_install_res.jar
C:\Program Files\MATLAB\R2014a\java\jar\ko_KR\student_activation_res.jar
C:\Program Files\MATLAB\R2014a\java\jar\ko_KR\web_connectivity_res.jar
C:\Program Files\MATLAB\R2014a\java\jar\lmlogin.jar
C:\Program Files\MATLAB\R2014a\java\jar\mde.jar
C:\Program Files\MATLAB\R2014a\java\jar\hg.jar
C:\Program Files\MATLAB\R2014a\java\jar\ide.jar
C:\Program Files\MATLAB\R2014a\java\jar\toolbox\matlab\guide.jar
C:\Program Files\MATLAB\R2014a\java\jar\page.jar
C:\Program Files\MATLAB\R2014a\java\jar\matlab.jar
C:\Program Files\MATLAB\R2014a\java\jar\jmi.jar
C:\Program Files\MATLAB\R2014a\java\jar\services.jar
C:\Program Files\MATLAB\R2014a\java\jar\widgets.jar
C:\Program Files\MATLAB\R2014a\java\jar\mlservices.jar
C:\Program Files\MATLAB\R2014a\java\jar\timer.jar
C:\Program Files\MATLAB\R2014a\java\jar\fatalexit.jar
C:\Program Files\MATLAB\R2014a\java\jar\mvm.jar
C:\Program Files\MATLAB\R2014a\java\jar\project\api.jar
C:\Program Files\MATLAB\R2014a\java\jar\project\impl.jar
C:\Program Files\MATLAB\R2014a\java\jar\mlwidgets.jar
C:\Program Files\MATLAB\R2014a\java\jarext\webservices\mcr_dws_client\mcr_dws_client.jar
C:\Program Files\MATLAB\R2014a\java\jarext\webservices\mwlic_client\mw-license-server-client.jar
C:\Program Files\MATLAB\R2014a\java\jar\util.jar
C:\Program Files\MATLAB\R2014a\java\jar\common.jar
C:\Program Files\MATLAB\R2014a\java\jar\mwswing.jar
C:\Program Files\MATLAB\R2014a\java\jar\beans.jar
C:\Program Files\MATLAB\R2014a\java\jar\mwt.jar
C:\Program Files\MATLAB\R2014a\java\jar\xml.jar
C:\Program Files\MATLAB\R2014a\java\jar\desktop.jar
C:\Program Files\MATLAB\R2014a\java\jar\toolstrip.jar
C:\Program Files\MATLAB\R2014a\java\jar\org\netbeans.jar
C:\Program Files\MATLAB\R2014a\java\jar\org\openide.jar
C:\Program Files\MATLAB\R2014a\java\jarext\saxon.jar
C:\Program Files\MATLAB\R2014a\java\jarext\helpsearch.jar
C:\Program Files\MATLAB\R2014a\java\jar\help\helpui.jar
C:\Program Files\MATLAB\R2014a\java\jar\html.jar
C:\Program Files\MATLAB\R2014a\java\jarext\search.jar
C:\Program Files\MATLAB\R2014a\java\jar\toolbox\optim.jar
C:\Program Files\MATLAB\R2014a\java\jar\resources\parallel_res.jar
C:\Program Files\MATLAB\R2014a\java\jar\toolbox\parallel\util.jar
C:\Program Files\MATLAB\R2014a\java\jar\toolbox\parallel\pctutil.jar
C:\Program Files\MATLAB\R2014a\java\jar\product.jar
C:\Program Files\MATLAB\R2014a\java\jar\activationclient.jar
C:\Program Files\MATLAB\R2014a\java\jar\deactivation.jar
C:\Program Files\MATLAB\R2014a\java\jar\vrd.jar
C:\Program Files\MATLAB\R2014a\java\jar\publishparser.jar
C:\Program Files\MATLAB\R2014a\java\jar\resource_core.jar
C:\Program Files\MATLAB\R2014a\java\jar\toolbox\rptgen.jar
C:\Program Files\MATLAB\R2014a\java\jar\toolbox\rptgenxmlcomp.jar
C:\Program Files\MATLAB\R2014a\java\jar\toolbox\shared\controllib.jar
C:\Program Files\MATLAB\R2014a\java\jar\toolbox\dastudio.jar
C:\Program Files\MATLAB\R2014a\java\jar\toolbox\shared\hwconnectinstaller\util.jar
C:\Program Files\MATLAB\R2014a\java\jar\toolbox\shared\hwconnectinstaller\common.jar
C:\Program Files\MATLAB\R2014a\java\jar\instutil.jar
C:\Program Files\MATLAB\R2014a\java\jar\toolbox\rptgencore.jar
C:\Program Files\MATLAB\R2014a\java\jar\toolbox\testmeas.jar
C:\Program Files\MATLAB\R2014a\java\jar\toolbox\stats.jar
C:\Program Files\MATLAB\R2014a\java\jar\storage\gdsinmatlab.jar
C:\Program Files\MATLAB\R2014a\java\jar\storage\gds.jar
C:\Program Files\MATLAB\R2014a\java\jar\storage\provider.jar
C:\Program Files\MATLAB\R2014a\java\jar\storage\motw.jar
C:\Program Files\MATLAB\R2014a\java\jar\storage\filesystemadapter.jar
C:\Program Files\MATLAB\R2014a\java\jar\activation.jar
C:\Program Files\MATLAB\R2014a\java\jar\toolbox\symbolic.jar
C:\Program Files\MATLAB\R2014a\java\jar\toolbox\timeseries.jar
C:\Program Files\MATLAB\R2014a\java\jar\webintegration.jar
C:\Program Files\MATLAB\R2014a\java\jar\mlwebservices.jar
C:\Program Files\MATLAB\R2014a\java\jar\net.jar
C:\Program Files\MATLAB\R2014a\java\jar\webproxy.jar
C:\Program Files\MATLAB\R2014a\java\jarext\mwaws_client.jar
C:\Program Files\MATLAB\R2014a\java\jarext\dws_client.jar
C:\Program Files\MATLAB\R2014a\java\jarext\webservices\loginws_client.jar
C:\Program Files\MATLAB\R2014a\java\jarext\webservices\service_request_client.jar
C:\Program Files\MATLAB\R2014a\java\jarext\webservices\dws_client.jar
C:\Program Files\MATLAB\R2014a\java\jarext\webservices\ws_client_core\mw-service-client-core.jar
C:\Program Files\MATLAB\R2014a\java\jarext\webservices\ws_usagedata_client\usagedata-client.jar
C:\Program Files\MATLAB\R2014a\java\jar\zh_CN\activation_res.jar
C:\Program Files\MATLAB\R2014a\java\jar\zh_CN\install_api_res.jar
C:\Program Files\MATLAB\R2014a\java\jar\zh_CN\professional_activation_res.jar
C:\Program Files\MATLAB\R2014a\java\jar\zh_CN\shared_install_res.jar
C:\Program Files\MATLAB\R2014a\java\jar\zh_CN\student_activation_res.jar
C:\Program Files\MATLAB\R2014a\java\jar\zh_CN\web_connectivity_res.jar
C:\Users\Public\Documents\MATLAB\bioformats_package.jar
DYNAMIC JAVA PATH
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