openmicroscopy/bioformats — pull request #217 by ctrueden (2012-11-14 20:37:00+00:00)
Title: Prairie fixes

This branch includes two improvements to the Prairie reader:

#### Partial dataset handling

It seems that PrairieView is capable of producing partial datasets. In particular, we received some sample data that is missing both channels of the last focal plane of the last time point. To handle such cases more robustly, we now pad the image count so that the ZCT product will match, and then return 0-filled planes for any missing files.

Test data for the partial datasets issue can be found at:

prairie/julie/bill-bement

For example:

prairie/julie/bill-bement/3/TSeries-10092012-1446-001

#### Multiple stage positions

PrairieView is capable of acquiring multiple stage positions (i.e., multiple Images), but does not differentiate them in the metadata in any way. Rather, all time points at all positions are simply numbered sequentially as "cycles" and conflated.

However, we can disentangle stage positions from time points after the fact by comparing stage positions. If we notice a repeating pattern of stage positions, we update the core metadata to reflect that fact.

Test data for the multiple stage position issue can be found at:

prairie/kristin/sampleset-001