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<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 "spim.io". 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">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>
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