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<div class="moz-cite-prefix">Hi Curtis,<br>
<br>
I have the first running version of a CellH5Reader (tested with
ImageInfo). I had problems setting up v4.4.7 in Eclipse, so I
settled for the current master branch (v4.4.6), which works nicely
together with Eclipse. I hope this will not hinder merging later
on. <br>
<br>
My next steps and questions are:<br>
<br>
* generate a small test CellH5 file. What is a reasonably size for
a such a file? I don't wonna burst your git repo with huge binary
data...<br>
* extend my test cases<br>
* extend the entries in coreMetaData. Is there a list of all
fields required to be meet the OME standards?<br>
* test the reader as a Fiji plug-in. Can you give me some
directions how to proceed from here?<br>
<br>
CellH5 also stores segmentations and object measurements. Is there
a way to loop through such information to Fiji using the Reader
class? For segmentations, I thought of either adding them as
separate channels or as another series. What is the preferred way?<br>
<br>
Thanks for all you help so far!<br>
<br>
Cheers,<br>
Christoph<br>
<br>
<br>
</div>
<blockquote
cite="mid:CADN69y=LYzQTucKRvxLKxDFj9J_LM_XimrH+JzwQtFDo25Dxdg@mail.gmail.com"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
<div dir="ltr">Hi Christophe,
<div><br>
</div>
<div>
<div>> I am new to Java and Maven so I followed
instructions from</div>
<div>> <a moz-do-not-send="true"
href="http://loci.wisc.edu/bio-formats/developing-bio-formats">http://loci.wisc.edu/bio-formats/developing-bio-formats</a>.
Using Eclipse</div>
<div>> (3.7 Indigo) I am unable to run the tests. I guess I
haven't set up</div>
<div>> the project properly.</div>
</div>
<div><br>
</div>
<div style="">Actually, the probelm is that the Eclipse support
was recently broken on the develop branch. There is a PR in
progress to make it work again [1]. For stability, you may
want to consider developing your reader against the v4.4.7
release tag [2] instead of using develop.</div>
<div style=""><br>
</div>
<div style="">
<div>> Where is the correct place to put a unit test case
for the new reader</div>
<div>> class?</div>
<div><br>
</div>
<div style="">The Bio-Formats convention is to use the same
package name as the reader class, but in the test/ subtree
rather than src/.</div>
<div style=""><br>
</div>
<div style="">But really, you can develop your own reader
however you want outside of the core Bio-Formats source. You
can even instantiate an ImageReader that includes your
reader in addition to the normal ones [4]. What you cannot
do at the moment -- although it is one of the benefits of
the SCIFIO refactoring [3] -- is have your reader get
automatically discovered and used when it is present on the
classpath. Of course, if you are planning to contribute your
reader to the core Bio-Formats distribution, this is a
non-issue.</div>
<div><br>
</div>
</div>
<div style="">Regards,</div>
<div style="">Curtis</div>
<div style=""><br>
</div>
<div style="">[1] <a moz-do-not-send="true"
href="https://github.com/openmicroscopy/bioformats/pull/480">https://github.com/openmicroscopy/bioformats/pull/480</a></div>
<div class="gmail_extra">[2] <a moz-do-not-send="true"
href="https://github.com/openmicroscopy/bioformats/tree/v4.4.7">https://github.com/openmicroscopy/bioformats/tree/v4.4.7</a></div>
<div class="gmail_extra">[3] <a moz-do-not-send="true"
href="https://github.com/hinerm/bioformats">https://github.com/hinerm/bioformats</a></div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">[4] For example:</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">
<div class="gmail_extra">import java.io.IOException;</div>
<div class="gmail_extra">
import loci.formats.ClassList;</div>
<div class="gmail_extra">import loci.formats.FormatException;</div>
<div class="gmail_extra">import loci.formats.FormatReader;</div>
<div class="gmail_extra">import loci.formats.IFormatReader;</div>
<div class="gmail_extra">import loci.formats.ImageReader;</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">public class CustomReader {</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra"><span class=""
style="white-space:pre"> </span>public static void
main(final String[] args) throws Exception {</div>
<div class="gmail_extra"><span class=""
style="white-space:pre"> </span>final
ClassList<IFormatReader> cl =
ImageReader.getDefaultReaderClasses();</div>
<div class="gmail_extra"><span class=""
style="white-space:pre"> </span>cl.addClass(MyReader.class);</div>
<div class="gmail_extra"><span class=""
style="white-space:pre"> </span>final ImageReader reader
= new ImageReader(cl);</div>
<div class="gmail_extra"><span class=""
style="white-space:pre"> </span>reader.setId("/path/to/test.data");</div>
<div class="gmail_extra"><span class=""
style="white-space:pre"> </span>// etc.</div>
<div class="gmail_extra"><span class=""
style="white-space:pre"> </span>}</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">
<span class="" style="white-space:pre"> </span>public
static class MyReader extends FormatReader {</div>
<div class="gmail_extra"><span class=""
style="white-space:pre"> </span>public MyReader() {</div>
<div class="gmail_extra">
<span class="" style="white-space:pre"> </span>super("My
File Format", ".mySuffix");</div>
<div class="gmail_extra"><span class=""
style="white-space:pre"> </span>}</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra"><span class=""
style="white-space:pre"> </span>@Override</div>
<div class="gmail_extra"><span class=""
style="white-space:pre"> </span>public byte[]
openBytes(final int no, final byte[] buf, final int x,</div>
<div class="gmail_extra"><span class=""
style="white-space:pre"> </span>final int y, final int w,
final int h) throws FormatException,</div>
<div class="gmail_extra"><span class=""
style="white-space:pre"> </span>IOException</div>
<div class="gmail_extra"><span class=""
style="white-space:pre"> </span>{</div>
<div class="gmail_extra"><span class=""
style="white-space:pre"> </span>// TODO Auto-generated
method stub</div>
<div class="gmail_extra"><span class=""
style="white-space:pre"> </span>return null;</div>
<div class="gmail_extra"><span class=""
style="white-space:pre"> </span>}</div>
<div class="gmail_extra"><span class=""
style="white-space:pre"> </span>}</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">}</div>
<div class="gmail_extra"><br>
</div>
<br>
<div class="gmail_quote">On Thu, Apr 25, 2013 at 8:33 AM,
Christoph Sommer <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:christoph.sommer@imba.oeaw.ac.at"
target="_blank">christoph.sommer@imba.oeaw.ac.at</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">Dear
Melissa,<br>
<br>
thanks for the fast reply!
<div class="im"><br>
<blockquote class="gmail_quote" style="margin:0px 0px
0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">The
develop branch of <a moz-do-not-send="true"
href="https://github.com/openmicroscopy/bioformats"
target="_blank">https://github.com/openmicroscopy/bioformats</a>
should compile and pass all tests. What sort of
development environment are you using? How are you
compiling and running tests?<br>
<blockquote class="gmail_quote" style="margin:0px 0px
0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">What
HDF5 library for Java would you recommend for native
hdf5<br>
access? To write these files (currently from Python)
I we HDF5 1.8.7<br>
</blockquote>
</blockquote>
</div>
I am new to Java and Maven so I followed instructions from
<a moz-do-not-send="true"
href="http://loci.wisc.edu/bio-formats/developing-bio-formats"
target="_blank">http://loci.wisc.edu/bio-formats/developing-bio-formats</a>.
Using Eclipse (3.7 Indigo) I am unable to run the tests. I
guess I haven't set up the project properly... I attached
the output I get in the eclipse console running "maven
build" (eclipse_build_output.txt). Somehow Eclipse cannot
resolve "import loci.formats.meta.MetadataStore;"<br>
<br>
Running Maven from the command line executes the tests and
it looks promising. Only 4 test in SCIFIO fail. I attached
the surefire html report... here's the console output.<br>
<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
-------------------------------------------------------<br>
T E S T S<br>
-------------------------------------------------------<br>
Running TestSuite<br>
[Parser] [WARN] Unknown value of attribute 'parallel' at
suite level: '@PARALLEL@'.<br>
Tests run: 954, Failures: 4, Errors: 0, Skipped: 0, Time
elapsed: 1,302.851 sec <<< FAILURE!<br>
<br>
Results :<br>
<br>
Failed tests: testIsDirectory(<a moz-do-not-send="true"
href="http://ome.scifio.io" target="_blank">ome.scifio.io</a>.utests.LocationTest):
bio-formats expected:<true> but was:<false><br>
testIsFile(<a moz-do-not-send="true"
href="http://ome.scifio.io" target="_blank">ome.scifio.io</a>.utests.LocationTest):
bio-formats expected:<false> but was:<true><br>
testIsHidden(<a moz-do-not-send="true"
href="http://ome.scifio.io" target="_blank">ome.scifio.io</a>.utests.LocationTest):
.hiddenTest1218465869181829460.tmp
expected:<false> but was:<true><br>
testToURL(<a moz-do-not-send="true"
href="http://ome.scifio.io" target="_blank">ome.scifio.io</a>.utests.LocationTest):
validTest5911385117004500129.tmp
expected:<<a class="moz-txt-link-freetext" href="file:/C:/Users/sommerc/AppData/Local/Temp/1366896587552-locat">file:/C:/Users/sommerc/AppData/Local/Temp/1366896587552-locat</a><br>
est5911385117004500129.tmp> but
was:<a class="moz-txt-link-rfc2396E" href="file://C:/Users/sommerc/AppData/Local/Temp/1366896587552-location-test/validTest5911385117004500129.tmp"><file://C:/Users/sommerc/AppData/Local/Temp/1366896587552-location-test/validTest5911385117004500129.tmp></a><br>
<br>
Tests run: 954, Failures: 4, Errors: 0, Skipped: 0<br>
<br>
[INFO] ------------------------------------------------------------------------<br>
[INFO] Reactor Summary:<br>
[INFO]<br>
[INFO] Bio-Formats projects
.............................. SUCCESS [1.413s]<br>
[INFO] JAI Image I/O Tools
............................... SUCCESS [1.720s]<br>
[INFO] MDB Tools (Java port)
............................. SUCCESS [0.450s]<br>
[INFO] SCIFIO-devel ......................................
FAILURE [21:43.630s]<br>
[INFO] Loci-Legacy .......................................
SKIPPED<br>
[INFO] Apache Jakarta POI ................................
SKIPPED<br>
[INFO] Luratech LuraWave stubs
........................... SKIPPED<br>
[INFO] OME-XML Java library
.............................. SKIPPED<br>
[INFO] libjpeg-turbo Java bindings
....................... SKIPPED<br>
[INFO] SCIFIO ............................................
SKIPPED<br>
[INFO] Bio-Formats code generator
........................ SKIPPED<br>
[INFO] Metakit ...........................................
SKIPPED<br>
[INFO] Bio-Formats library
............................... SKIPPED<br>
[INFO] LOCI Common compatibility JAR
..................... SKIPPED<br>
[INFO] LOCI Plugins for ImageJ
........................... SKIPPED<br>
[INFO] LOCI Tools bundle .................................
SKIPPED<br>
[INFO] OME I/O ...........................................
SKIPPED<br>
[INFO] OME Plugins for ImageJ
............................ SKIPPED<br>
[INFO] OME Tools bundle ..................................
SKIPPED<br>
[INFO] SCIFIO ............................................
SKIPPED<br>
[INFO] LOCI testing framework
............................ SKIPPED<br>
[INFO] XSD-FU ............................................
SKIPPED<br>
[INFO] ------------------------------------------------------------------------<br>
[INFO] BUILD FAILURE<br>
[INFO] ------------------------------------------------------------------------<br>
[INFO] Total time: 21:48.070s<br>
[INFO] Finished at: Thu Apr 25 15:29:48 CEST 2013<br>
[INFO] Final Memory: 22M/440M<br>
[INFO] ------------------------------------------------------------------------<br>
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.12:test
(default-test) on project scifio-devel: There are<br>
[...]<br>
<br>
</blockquote>
Btw. Where is the correct place to put a unit test case
for the new reader class?<br>
<br>
Cheers,<br>
Christoph<br>
<br>
<br>
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href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel"
target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><br>
<br>
</blockquote>
</div>
<br>
</div>
</div>
</blockquote>
<br>
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