<html>
<head>
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
</head>
<body text="#000000" bgcolor="#FFFFFF">
<p>Dear Stephan and OpenSpim users,</p>
<p>thanks for pointing me to the autoloader. I tested it on our data
and technically it works! It seems tiles and angles are still
mistaken, but this seems to be a problem of the wrong meta data...
I now work on automating the MVR process for our setup.<br>
</p>
<p>Also, we found a way to truncate the containing ome-xml data, to
make each output files 'stand-alone' for specific cases. Yet, the
autoloader is my preferred solution.</p>
<p>Thanks to all for your help!</p>
<p>Cheers,</p>
<p>Chris<br>
</p>
<br>
<div class="moz-cite-prefix">Am 11/7/2017 um 8:17 PM schrieb
<a class="moz-txt-link-abbreviated" href="mailto:Stephan.Preibisch@mdc-berlin.de">Stephan.Preibisch@mdc-berlin.de</a>:<br>
</div>
<blockquote type="cite"
cite="mid:60858A62-F207-4ED3-8837-DA7A9774127C@mdc-berlin.de">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
Hi, did you try using the Autoloader of the MVR/BigStitcher (it’s
basically the same now) for import? Activate the BigStitcher
update site first to get the newest code. It should handle
OME-TIff ... if not, send us a small example and we’ll fix it.<br>
<br>
Cheers,
<div>Stephan </div>
<div><br>
<div id="AppleMailSignature">Sent from my iPhone</div>
<div><br>
On Nov 7, 2017, at 16:17, Christoph Sommer <<a
href="mailto:christoph.sommer@ist.ac.at"
moz-do-not-send="true">christoph.sommer@ist.ac.at</a>>
wrote:<br>
<br>
</div>
<blockquote type="cite">
<div>
<p>Dear HongKee,</p>
thank so much for your recommendation and code. When I
understand correctly, it would require the deployment of
this VirtualStack class to all ImageJ instances of potential
users. I was hoping for a solution, which does not need
adaptions of ImageJ.<br>
<br>
Alternatively, we could create a different output format in
the acquisition (no multi-file OMETiff). I saw that there's
already a "IndividualImagesHandler" or an HDF5 handler in "<a
href="http://spim.io" moz-do-not-send="true">spim.io</a>".
Does someone have experience with alternative output
formats?<br>
<br>
Cheers,<br>
Chris<br>
<br>
<br>
<blockquote type="cite"
cite="mid:4E099AE3-253B-4B13-8C7F-995E35B5A6B1@mpi-cbg.de">
<div class="">We have also faced those problems because
the default image opener is trying to get the metadata
for every file.</div>
<div class="">I really recommend you to make own
ImageStack class for reading the metadata just once for
your whole series.</div>
<div class=""><br class="">
</div>
<div class="">We had to create our version of VirtualStack
class based on <a
href="https://imagej.nih.gov/ij/plugins/virtual-opener.html"
class="" moz-do-not-send="true">
https://imagej.nih.gov/ij/plugins/virtual-opener.html</a> to
avoid redundant metadata reading. The below code is not
a perfect version, please, use it as a reference.</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">Hopefully, it will help you.</div>
<div class=""><br class="">
</div>
<div class="">Cheers,</div>
<div class="">HongKee</div>
</div>
<div class=""><br class="">
</div>
<div class="">———————————————————</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">import ij.ImageStack;</div>
<div class="">import ij.process.ByteProcessor;</div>
<div class="">import ij.process.ImageProcessor;</div>
<div class="">import loci.formats.FormatException;</div>
<div class="">import loci.formats.ImageReader;</div>
<div class="">import
loci.plugins.util.ImageProcessorReader;</div>
</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">import
loci.common.services.DependencyException;</div>
<div class="">import
loci.common.services.ServiceException;</div>
<div class="">import
loci.common.services.ServiceFactory;</div>
<div class="">import loci.formats.FormatException;</div>
<div class="">import loci.formats.ImageReader;</div>
<div class="">import loci.formats.meta.IMetadata;</div>
<div class="">import
loci.formats.services.OMEXMLService;</div>
</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">public class MyImageStack extends
ImageStack</div>
<div class="">{</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>private
int bitDepth;</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>private
int width, height;</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>ImageProcessorReader
imageProcessorReader;</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>private
int zSize = 1, tSize = 1, cSize = 1;</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>private
int cEffectiveSize = 1;</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>public
void addSlice( String path )</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>{</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>if(path !=
null)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>{</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>if(width
== 0)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>{</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>//
create format reader</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>ImageReader
reader = getImageReader( path );</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>//
output dimensional information</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>int
sizeX = reader.getSizeX();</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>this.width
= sizeX;</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>int
sizeY = reader.getSizeY();</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>this.height
= sizeY;</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>//
System.out.println("Effective C" +
reader.getEffectiveSizeC());</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>setcEffectiveSize(
reader.getEffectiveSizeC() );</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>int
sizeC = reader.getSizeC();</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>int
sizeZ = reader.getSizeZ();</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>int
sizeT = reader.getSizeT();</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>//
System.out.println( "C=" + sizeC + " Z=" + sizeZ + "
T=" + sizeT );</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>setcSize(
sizeC );</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>setzSize(
sizeZ );</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>settSize(
sizeT );</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>this.bitDepth
= reader.getBitsPerPixel();</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>this.imageProcessorReader
= new ImageProcessorReader( reader );</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>}</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>}</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>}</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>public
ImageProcessor getProcessor(int n) </div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>{</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>//
properly implement to get ImageProcessor based on n</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>}</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>public
static ImageReader getImageReader( String path )</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>{</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>ImageReader
reader = null;</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>try</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>{</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>ServiceFactory
factory = new ServiceFactory();</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>OMEXMLService
service = factory.getInstance(OMEXMLService.class);</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>IMetadata
meta = service.createOMEXMLMetadata();</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>//
create format reader</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>reader
= new ImageReader();</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>reader.setMetadataStore(meta);</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>//
initialize file</div>
<div class="">//<span class="Apple-tab-span" style="white-space:pre"> </span>System.out.println(path);</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>reader.setId(
path );</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>}</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>catch
( DependencyException e )</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>{</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>e.printStackTrace();</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>}</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>catch
( ServiceException e )</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>{</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>e.printStackTrace();</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>}</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>catch
( IOException e )</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>{</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>e.printStackTrace();</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>}</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>catch
( FormatException e )</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>{</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>e.printStackTrace();</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>}</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>return
reader;</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>}</div>
<div class="">}</div>
</div>
<div class=""><br class="">
</div>
<div class="">———————————————</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On Nov 6, 2017, at 10:43 AM, Christoph
Sommer <<a
href="mailto:christoph.sommer@ist.ac.at"
class="" moz-do-not-send="true">christoph.sommer@ist.ac.at</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="">Dear OpenSpim folks,<br class="">
<br class="">
thanks for creating such a great resource!<br
class="">
<br class="">
We are currently using an OpenSpim setup and the
created output is a multi-file ome-tiff. For
many applications (e.g. the MVR from Stephan
Preibisch et al.) we need to convert the
ome-tiff to normal tiff.<br class="">
<br class="">
Unfortunately, for long time-lapse the
conversion takes forever, since for each
conversion step all meta-data is parsed from
each single time point. My script uses the
Bioformats ImporterOptions class, but I can't
see how I can bypass the meta-data parsing. I
also tried the 'bvconvert' command line script
but also got issues there. Also reading from
Python (e.g. with the module 'tifffile' only
return always the first angle image-stack...)<br
class="">
<br class="">
Would you have any idea?<br class="">
<br class="">
Cheers,<br class="">
<br class="">
Chris<br class="">
<br class="">
<br class="">
_______________________________________________<br
class="">
OpenSPIM mailing list<br class="">
<a href="mailto:OpenSPIM@openspim.org" class=""
moz-do-not-send="true">OpenSPIM@openspim.org</a><br
class="">
<a class="moz-txt-link-freetext"
href="http://openspim.org/mailman/listinfo/openspim"
moz-do-not-send="true">http://openspim.org/mailman/listinfo/openspim</a><br
class="">
</div>
</div>
</blockquote>
</div>
<br class="">
<div class="">
<div style="color: rgb(0, 0, 0); letter-spacing:
normal; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space:
normal; widows: auto; word-spacing: 0px;
-webkit-text-stroke-width: 0px; word-wrap:
break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space;" class="">
<div style="color: rgb(0, 0, 0); letter-spacing:
normal; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none;
white-space: normal; widows: auto; word-spacing:
0px; -webkit-text-stroke-width: 0px; word-wrap:
break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space;" class="">
<br class="">
--<br class="">
HongKee Moon<br class="">
Scientific Software Engineer<br class="">
Scientific Computing Facility<br class="">
<br class="">
Max Planck Institute of Molecular Cell Biology and
Genetics<br class="">
Pfotenhauerstr. 108<br class="">
01307 Dresden<br class="">
Germany<br class="">
<br class="">
fon: +49 351 210 1923<br class="">
fax: +49 351 210 1907<br class="">
<a href="http://www.mpi-cbg.de" class=""
moz-do-not-send="true">www.mpi-cbg.de</a></div>
</div>
</div>
<br class="">
</div>
</blockquote>
<br>
</div>
</blockquote>
<blockquote type="cite">
<div><span>_______________________________________________</span><br>
<span>OpenSPIM mailing list</span><br>
<span><a href="mailto:OpenSPIM@openspim.org"
moz-do-not-send="true">OpenSPIM@openspim.org</a></span><br>
<span><a
href="http://openspim.org/mailman/listinfo/openspim"
moz-do-not-send="true">http://openspim.org/mailman/listinfo/openspim</a></span><br>
</div>
</blockquote>
</div>
</blockquote>
<br>
</body>
</html>