Bug: ExporterI is missing call to FormatTools.getZCTCoords

[jamoore]

From Melissa:

[There] looks to be a problem in ExporterI, lines 351-357. Near as I can tell, the 'reader' object's dimension order matches that of the original file, but the 'writer' object's dimension order is always XYZCT. Thus, the dimension order of the exported OME-TIFF doesn't necessarily match the ordering of the planes. I think the problem can be solved by changing lines 355-356 from this:

 reader.openBytes(i, plane);
 writer.saveBytes(i, plane);

to this:

 int[] zct = FormatTools.getZCTCoords(
   retrieve.getPixelsDimensionOrder(0).getValue(),
   reader.getSizeZ(), reader.getSizeC(), reader.getSizeT(), planeCount, i);
 int readerIndex = reader.getIndex(zct[0], zct[1], zct[2]);
 reader.openBytes(readerIndex, plane);
 writer.saveBytes(i, plane);

See

[jmoore]

(In [8814/omero]) Adding getZCTCoords to ExporterI Reader usage (See #3718)

[jmoore]

Fixed in trunk. Will backport to source:branches/Beta4.2 momentarily.

[jmoore]

(In [8867/omero]) Adding getZCTCoords to ExporterI Reader usage (See #3718)

original-svn-id: ​file:///home/svn/omero/trunk@8814 05709c45-44f0-0310-885b-81a1db45b4a6

[Chris Allan <callan@…>]

(In [bd43082c72a4079add928031fa270dc7e6dc6bdf/ome.git]) Enforce XYZCT dimension order. (Fixes #3124)

In order to ensure that the changes made in ([8867/omero]) (See #3718)
remain valid and that exports have the correct dimension order (Closes
order set in the OMERO database. The server relies on an XYZCT order and
all interactions happen as such, it must be enforced throughout.

[Chris Allan <callan@…>]

(In [c60d1c673de9ece42501b7b5709ccaeeada99c70/ome.git] on branch dev_4_2) Enforce XYZCT dimension order. (Fixes #3124)

In order to ensure that the changes made in ([8867/omero]) (See #3718)
remain valid and that exports have the correct dimension order (Closes
order set in the OMERO database. The server relies on an XYZCT order and
all interactions happen as such, it must be enforced throughout.
(cherry picked from commit bd43082c72a4079add928031fa270dc7e6dc6bdf)