[ome-users] [OME] #12420: Bug: MIPAV importer plugin broken due to model changes

[Dr. Pascal Detampel]

Just in case somebody runs into the same issue.
With the help of Roger, and some digging in the corresponding classes, I got it to work again.

Next to replacing getDimensions to getPixels, dropping the index, and changing the object type to PositiveFloat (thanks Roger), I had to call the method *.getValue() instead of *.floatValue() and change the type from float to double in the lines below. Only the object "dimTimeInc” should be Double and the elements of the array “res” (a few lines below) have to be casted (float). In addition, the object type PositiveFloat has to be imported at the top of the file (import ome.xml.model.primitives.PositiveFloat;).

Except for the import statement at the top, my changes looked like the following:

>          // harvest physical resolution
>          PositiveFloat dimPhysSizeX = store.getPixelsPhysicalSizeX(0);
>          PositiveFloat dimPhysSizeY = store.getPixelsPhysicalSizeY(0);
>          PositiveFloat dimPhysSizeZ = store.getPixelsPhysicalSizeZ(0);
>          Double dimTimeInc = store.getPixelsTimeIncrement(0);
>          double physSizeX = dimPhysSizeX == null ?
>            1.0f : dimPhysSizeX.getValue();
>          double physSizeY = dimPhysSizeY == null ?
>            1.0f : dimPhysSizeY.getValue();
>          double physSizeZ = dimPhysSizeZ == null ?
>            1.0f : dimPhysSizeZ.getValue();
>          float timeInc = dimTimeInc == null ? 1.0f : dimTimeInc.floatValue();
> 
>          // compute dimensional extents
>          int[] dimExtents = {sizeX, sizeY, sizeZ, sizeT};
>          float[] res = {(float) physSizeX, (float) physSizeY, (float) physSizeZ, timeInc};
>          int[] units = {
>            FileInfoBase.MICROMETERS, FileInfoBase.MICROMETERS,
>            FileInfoBase.MICROMETERS, FileInfoBase.SECONDS
>          };

Maybe there is an more elegant way, but at least it compiles again and Mipav shows the BioFormatsImporter under Plugins.
But with respect to Zeiss czi stacks, the importer throws an error message that “An I/O error occurred reading the file: Import data error: bounds incorrect”.
So I guess, as already pointed out by Roger, the code has some additional problems.

Thanks,
Pascal


On Jun 27, 2014, at 7:42 AM, OME <trac at cvs.openmicroscopy.org.uk> wrote:

> #12420: Bug: MIPAV importer plugin broken due to model changes
> ------------------------------+---------------------------------------------
>      Reporter:  rleigh       |        Owner:  mlinkert   
>          Type:  task         |       Status:  new        
>      Priority:  minor        |    Milestone:  Unscheduled
>     Component:  Bio-Formats  |      Version:  5.0.2      
>    Resolution:               |     Keywords:             
> Remaining Time:               |       Sprint:             
>     Resources:               |   References:             
> Referenced By:               |  
> ------------------------------+---------------------------------------------
> PlugInBioFormatsImporter.java will not compile:
> 
> {{{
> labtop:plugins pascal$ javac -cp
> /Applications/mipav:/Applications/mipav/bioformats_package.jar
> PlugInBioFormatsImporter.java
> 
> PlugInBioFormatsImporter.java:201: cannot find symbol
> symbol  : method getDimensionsPhysicalSizeX(int,int)
> location: interface loci.formats.meta.IMetadata
>           Float dimPhysSizeX = store.getDimensionsPhysicalSizeX(0, 0);
> 
> PlugInBioFormatsImporter.java:202: cannot find symbol
> symbol  : method getDimensionsPhysicalSizeY(int,int)
> location: interface loci.formats.meta.IMetadata
>           Float dimPhysSizeY = store.getDimensionsPhysicalSizeY(0, 0);
> 
> PlugInBioFormatsImporter.java:203: cannot find symbol
> symbol  : method getDimensionsPhysicalSizeZ(int,int)
> location: interface loci.formats.meta.IMetadata
>           Float dimPhysSizeZ = store.getDimensionsPhysicalSizeZ(0, 0);
> 
> PlugInBioFormatsImporter.java:204: cannot find symbol
> symbol  : method getDimensionsTimeIncrement(int,int)
> location: interface loci.formats.meta.IMetadata
>           Float dimTimeInc = store.getDimensionsTimeIncrement(0, 0);
> 
> 4 errors
> }}}
> 
> The method calls in question were removed from the OME data model in 2010,
> and so it has been non-functional for some time.
> 
> Fixing the above error is simple (change getDimensions to getPixels and
> drop the pixel index).  However, there may be additional problems with the
> code.
> 
> Ideally, there should be a maven pom to allow this to be added to our
> regular CI infrastructure to pick up any future breakage.
> 
> -- 
> Ticket URL: <http://trac.openmicroscopy.org.uk/ome/ticket/12420>
> OME <http://www.openmicroscopy.org/>
> OME Project