fiji/fiji — pull request #3 by ctrueden (2012-04-20 19:17:39+00:00)
Title: Stitcher improvements

This branch contains some improvements to the Fiji Stitching plugin:

1. It adds support for stitching single-series data by treating each time point as a separate tile. I have an actual dataset like this (available upon request), which prompted this development. I looked into improving Bio-Formats to parse this dataset as multiple image series, but it would be very difficult to differentiate given that there is nothing in the metadata to indicate the data should be split this way. Rather, I thought it would be nice if the Fiji Stitching plugin made a best effort to perform the stitching for this sort of data, rather than simply failing with an error message.

2. It fixes a potential NPE when parsing physical pixel sizes.

3. It fixes a potential mismatch when parsing tile coordinates from Plane elements. The Plane elements may be out of order, with (C,Z,T)=(0,0,0) not necessarily corresponding to the first Plane element, so we must be a little more clever in how we parse them. See the HashMap called planeMap in Stitching_Grid.java for details.

4. A couple other very minor fixes.

I believe these changes only fix bugs, and introduce support for the single-series stitching using time points. Existing behavior otherwise should be unchanged.

@StephanPreibisch : If you could review at your convenience and merge if you like it, I would greatly appreciate it. If you see any issues with these changes, let's discuss.