[ome-devel] cellh5 reader for bio-formats
Christoph Sommer
christoph.sommer at imba.oeaw.ac.at
Sun Apr 28 12:37:45 BST 2013
Hi Curtis,
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.
My next steps and questions are:
* 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...
* extend my test cases
* extend the entries in coreMetaData. Is there a list of all fields
required to be meet the OME standards?
* test the reader as a Fiji plug-in. Can you give me some directions how
to proceed from here?
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?
Thanks for all you help so far!
Cheers,
Christoph
> Hi Christophe,
>
> > I am new to Java and Maven so I followed instructions from
> > http://loci.wisc.edu/bio-formats/developing-bio-formats. Using Eclipse
> > (3.7 Indigo) I am unable to run the tests. I guess I haven't set up
> > the project properly.
>
> 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.
>
> > Where is the correct place to put a unit test case for the new reader
> > class?
>
> The Bio-Formats convention is to use the same package name as the
> reader class, but in the test/ subtree rather than src/.
>
> 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.
>
> Regards,
> Curtis
>
> [1] https://github.com/openmicroscopy/bioformats/pull/480
> [2] https://github.com/openmicroscopy/bioformats/tree/v4.4.7
> [3] https://github.com/hinerm/bioformats
>
> [4] For example:
>
> import java.io.IOException;
> import loci.formats.ClassList;
> import loci.formats.FormatException;
> import loci.formats.FormatReader;
> import loci.formats.IFormatReader;
> import loci.formats.ImageReader;
>
> public class CustomReader {
>
> public static void main(final String[] args) throws Exception {
> final ClassList<IFormatReader> cl = ImageReader.getDefaultReaderClasses();
> cl.addClass(MyReader.class);
> final ImageReader reader = new ImageReader(cl);
> reader.setId("/path/to/test.data");
> // etc.
> }
>
> public static class MyReader extends FormatReader {
> public MyReader() {
> super("My File Format", ".mySuffix");
> }
>
> @Override
> public byte[] openBytes(final int no, final byte[] buf, final int x,
> final int y, final int w, final int h) throws FormatException,
> IOException
> {
> // TODO Auto-generated method stub
> return null;
> }
> }
>
> }
>
>
> On Thu, Apr 25, 2013 at 8:33 AM, Christoph Sommer
> <christoph.sommer at imba.oeaw.ac.at
> <mailto:christoph.sommer at imba.oeaw.ac.at>> wrote:
>
> Dear Melissa,
>
> thanks for the fast reply!
>
> The develop branch of
> https://github.com/openmicroscopy/bioformats should compile
> and pass all tests. What sort of development environment are
> you using? How are you compiling and running tests?
>
> What HDF5 library for Java would you recommend for native hdf5
> access? To write these files (currently from Python) I we
> HDF5 1.8.7
>
> I am new to Java and Maven so I followed instructions from
> http://loci.wisc.edu/bio-formats/developing-bio-formats. 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;"
>
> 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.
>
> -------------------------------------------------------
> T E S T S
> -------------------------------------------------------
> Running TestSuite
> [Parser] [WARN] Unknown value of attribute 'parallel' at suite
> level: '@PARALLEL@'.
> Tests run: 954, Failures: 4, Errors: 0, Skipped: 0, Time
> elapsed: 1,302.851 sec <<< FAILURE!
>
> Results :
>
> Failed tests: testIsDirectory(ome.scifio.io
> <http://ome.scifio.io>.utests.LocationTest): bio-formats
> expected:<true> but was:<false>
> testIsFile(ome.scifio.io
> <http://ome.scifio.io>.utests.LocationTest): bio-formats
> expected:<false> but was:<true>
> testIsHidden(ome.scifio.io
> <http://ome.scifio.io>.utests.LocationTest):
> .hiddenTest1218465869181829460.tmp expected:<false> but was:<true>
> testToURL(ome.scifio.io
> <http://ome.scifio.io>.utests.LocationTest):
> validTest5911385117004500129.tmp
> expected:<file:/C:/Users/sommerc/AppData/Local/Temp/1366896587552-locat
> est5911385117004500129.tmp> but
> was:<file://C:/Users/sommerc/AppData/Local/Temp/1366896587552-location-test/validTest5911385117004500129.tmp>
>
> Tests run: 954, Failures: 4, Errors: 0, Skipped: 0
>
> [INFO]
> ------------------------------------------------------------------------
> [INFO] Reactor Summary:
> [INFO]
> [INFO] Bio-Formats projects ..............................
> SUCCESS [1.413s]
> [INFO] JAI Image I/O Tools ...............................
> SUCCESS [1.720s]
> [INFO] MDB Tools (Java port) .............................
> SUCCESS [0.450s]
> [INFO] SCIFIO-devel ......................................
> FAILURE [21:43.630s]
> [INFO] Loci-Legacy ....................................... SKIPPED
> [INFO] Apache Jakarta POI ................................ SKIPPED
> [INFO] Luratech LuraWave stubs ........................... SKIPPED
> [INFO] OME-XML Java library .............................. SKIPPED
> [INFO] libjpeg-turbo Java bindings ....................... SKIPPED
> [INFO] SCIFIO ............................................ SKIPPED
> [INFO] Bio-Formats code generator ........................ SKIPPED
> [INFO] Metakit ........................................... SKIPPED
> [INFO] Bio-Formats library ............................... SKIPPED
> [INFO] LOCI Common compatibility JAR ..................... SKIPPED
> [INFO] LOCI Plugins for ImageJ ........................... SKIPPED
> [INFO] LOCI Tools bundle ................................. SKIPPED
> [INFO] OME I/O ........................................... SKIPPED
> [INFO] OME Plugins for ImageJ ............................ SKIPPED
> [INFO] OME Tools bundle .................................. SKIPPED
> [INFO] SCIFIO ............................................ SKIPPED
> [INFO] LOCI testing framework ............................ SKIPPED
> [INFO] XSD-FU ............................................ SKIPPED
> [INFO]
> ------------------------------------------------------------------------
> [INFO] BUILD FAILURE
> [INFO]
> ------------------------------------------------------------------------
> [INFO] Total time: 21:48.070s
> [INFO] Finished at: Thu Apr 25 15:29:48 CEST 2013
> [INFO] Final Memory: 22M/440M
> [INFO]
> ------------------------------------------------------------------------
> [ERROR] Failed to execute goal
> org.apache.maven.plugins:maven-surefire-plugin:2.12:test
> (default-test) on project scifio-devel: There are
> [...]
>
> Btw. Where is the correct place to put a unit test case for the
> new reader class?
>
> Cheers,
> Christoph
>
>
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