[ome-devel] cellh5 reader for bio-formats
Melissa Linkert
melissa at glencoesoftware.com
Mon Apr 29 14:43:59 BST 2013
Hi Christoph,
> 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...
We do not put test data in bioformats.git; the best thing to do is to
pick a representative set of test data (regardless of size) and make
them available elsewhere for testing.
> * extend my test cases
> * extend the entries in coreMetaData. Is there a list of all fields
> required to be meet the OME standards?
At a minimum: sizeX, sizeY, sizeZ, sizeC, sizeT, dimensionOrder, rgb,
pixelType, interleaved, littleEndian, indexed, and falseColor.
> * test the reader as a Fiji plug-in. Can you give me some directions
> how to proceed from here?
Rebuilding the jars with your reader and copying them into ImageJ/Fiji
should allow you to open CellH5 files just by clicking "Plugins > LOCI >
Bio-Formats Importer". In Fiji, make sure that the new jars completely
replace any existing Bio-Formats jars (e.g. jars/bio-formats*.jar,
jars/scifio-*.jar).
> 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?
If the segmentations and measurements are stored as images, then I would
suggest using a separate series to store them. If they are stored as
shape descriptions, then you may wish to use the OME-XML ROI model to
store them:
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2012-06/ROI_xsd.html#ROI
https://github.com/openmicroscopy/bioformats/blob/v4.4.7/components/scifio/src/loci/formats/meta/MetadataStore.java#L1681
Regards,
-Melissa
On Sun, Apr 28, 2013 at 01:37:45PM +0200, Christoph Sommer wrote:
> 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
> >
> >
> > _______________________________________________
> > ome-devel mailing list
> > ome-devel at lists.openmicroscopy.org.uk
> > <mailto:ome-devel at lists.openmicroscopy.org.uk>
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
> >
> >
>
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