[ome-users] [OME] #12420: Bug: MIPAV importer plugin broken due to model changes
Helen Flynn
h.flynn at dundee.ac.uk
Tue Jul 1 10:16:00 BST 2014
Dear Pascal,
The current plan is to fix this issue so that MIPAV works again for the upcoming 5.0.3 release of Bio-Formats. In the event we don't manage this, I will update the documentation to make people aware of the problem.
Regards,
Helen
Dr Helen Flynn
OME Technical Writer
Centre for Gene Regulation & Expression
Open Microscopy Environment
University of Dundee
http://openmicroscopy.org<http://openmicroscopy.org/>
On 28 Jun 2014, at 18:47, Curtis Rueden <ctrueden at wisc.edu<mailto:ctrueden at wisc.edu>> wrote:
Hi Pascal,
> Would it not be better to mention this in the current documentation that the
> present Bioformats Plugin is not any more supported for MIPAV?
I agree that updating the documentation is a good idea. However:
1) I do not control the documentation, so suggesting it to me in a private mail will not accomplish it. I have re-CCed the ome-users list.
2) Of course, I think it would be "better" to fix the plugin so that it actually works in MIPAV again.
Regards,
Curtis
On Sat, Jun 28, 2014 at 10:03 AM, Dr. Pascal Detampel <pdetampe at ucalgary.ca<mailto:pdetampe at ucalgary.ca>> wrote:
Hi Curtis,
Thanks for your reply.
Would it not be better to mention this in the current documentation that the present Bioformats Plugin is not any more supported for MIPAV?
Right now, one gets the impression that the installation is just straight forward.
I will be away till Wednesday.
Best,
Pascal
Am 28.06.2014 um 06:51 schrieb Curtis Rueden <ctrueden at wisc.edu<mailto:ctrueden at wisc.edu>>:
> Hi Pascal,
>
> > 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.
>
> The plan we discussed a couple of years ago with the MIPAV team was for them to adopt the plugin upstream as part of MIPAV. We did some work [1] to make it possible.
>
> But I guess it never panned out. If you are interested in seeing that happen you could write a mail to the MIPAV mailing list [2].
>
> Regards,
> Curtis
>
> [1] https://github.com/openmicroscopy/bioformats/pull/64
> [2] http://mipav.cit.nih.gov/pubwiki/index.php/MIPAV_mailing_list
>
>
> On Fri, Jun 27, 2014 at 10:14 PM, Dr. Pascal Detampel <pdetampe at ucalgary.ca<mailto:pdetampe at ucalgary.ca>> wrote:
> 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<mailto: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
>
>
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