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Task #6489 (closed)

Opened 13 years ago

Closed 13 years ago

Last modified 13 years ago

Bug: FileStitcher does not respect underlying reader

Reported by:	mlinkert	Owned by:	mlinkert
Priority:	major	Milestone:	OMERO-Beta4.3.2
Component:	Bio-Formats	Version:	n.a.
Keywords:	n.a.	Cc:	gbonamy@…
Resources:	n.a.	Referenced By:	n.a.
References:	n.a.	Remaining Time:	0.0d
Sprint:	2011-08-18 (3)

Description

For example:

  FileStitcher stitcher = new FileStitcher(new TiffReader());
  stitcher.setId(...);

The readers constructed by FileStitcher? will be ImageReaders?, not TiffReaders?. A partial work-around for this is in place, if you call stitcher.setReaderClassList(...), but this isn't ideal. The reader passed to the FileStitcher? constructor should be used as a template for constructing any additional readers.

References

Change History (10)

comment:1 Changed 13 years ago by mlinkert

The problem also apparently appears when using setReaderClassList(...), e.g.

ClassList<IFormatReader> classList = new ClassList<IFormatReader>(IFormatReader.class);
  if (path.getSystem().equals(ServeletCommonParameters.INSTRUMENTS[0][0]))
   classList.addClass(loci.formats.in.FlexReader.class);
  if (path.getSystem().equals(ServeletCommonParameters.INSTRUMENTS[1][0]))
   classList.addClass(loci.formats.in.MetamorphReader.class);
  classList.removeClass(IFormatReader.class);
  reader.setReaderClassList(classList);

I thought I had solved that problem previously, but evidently not.

comment:2 Changed 13 years ago by mlinkert

Sprint set to 2011-08-18 (3)

comment:3 Changed 13 years ago by Melissa Linkert <melissa@…>

(In [d12293424af305dba1c559a88997d8d2c2208232/bioformats.git]) Reset 'reader' so that the correct ClassList? is used.

See #6489.

comment:4 Changed 13 years ago by Melissa Linkert <melissa@…>

(In [d12293424af305dba1c559a88997d8d2c2208232/bioformats.git]) Reset 'reader' so that the correct ClassList? is used.

See #6489.

comment:5 Changed 13 years ago by Melissa Linkert <melissa@…>

Remaining Time set to 0
Resolution set to fixed
Status changed from new to closed

(In [80b31af07c7a2b18822fe2c2d07b4615cc3e4448/bioformats.git]) Set the ClassList? if a reader from loci.formats.in is passed to the constructor.

Closes #6489.

comment:6 Changed 13 years ago by Melissa Linkert <melissa@…>

(In [80b31af07c7a2b18822fe2c2d07b4615cc3e4448/bioformats.git]) Set the ClassList? if a reader from loci.formats.in is passed to the constructor.

Closes #6489.

comment:7 Changed 13 years ago by Melissa Linkert <melissa@…>

(In [1a81a5614bee880bfca9a358c0da64bba60c3fc5/bioformats.git]) Reset 'reader' so that the correct ClassList? is used.

See #6489.
(cherry picked from commit d12293424af305dba1c559a88997d8d2c2208232)

comment:8 Changed 13 years ago by Melissa Linkert <melissa@…>

(In [6c498894720c40fdc4b998c8e179049e2f43325e/bioformats.git]) Set the ClassList? if a reader from loci.formats.in is passed to the constructor.

Closes #6489.
(cherry picked from commit 80b31af07c7a2b18822fe2c2d07b4615cc3e4448)

comment:9 Changed 13 years ago by Melissa Linkert <melissa@…>

(In [1a81a5614bee880bfca9a358c0da64bba60c3fc5/bioformats.git]) Reset 'reader' so that the correct ClassList? is used.

See #6489.
(cherry picked from commit d12293424af305dba1c559a88997d8d2c2208232)

comment:10 Changed 13 years ago by Melissa Linkert <melissa@…>

(In [6c498894720c40fdc4b998c8e179049e2f43325e/bioformats.git]) Set the ClassList? if a reader from loci.formats.in is passed to the constructor.

Closes #6489.
(cherry picked from commit 80b31af07c7a2b18822fe2c2d07b4615cc3e4448)

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