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Add reader for Ventana .bif files #3336
Commits on Mar 29, 2019
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Progress on tile stitching for the full resolution image
Not done yet, as the overlaps are still not quite right. This is closer than the previous version with no overlap calculation though.
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Average a subset of recorded overlaps instead of using overlap list
A lot of trial and error indicates that the recorded overlap list for each AOI does not indicate the total number of overlaps to be removed. Individual overlap values are also sometimes incorrect by a significant amount. This takes the approach of averaging high-confidence overlaps to produce a single value for each of X and Y, which are then applied to all tiles in the AOI.
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Add "ventana.split_tiles" boolean option
The option is false by default; when set to true, each tile in the full resolution image is returned as a separate series. Lower resolutions are then ignored. This should make it easier to stitch tiles externally if needed.
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Ventana: adjust XY size to match AOI bounds
Conflicts: components/formats-gpl/src/loci/formats/in/VentanaReader.java
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Adjust XY coordinate calculation for low resolution tiles
Changing the rounding strategy results in smoother stitching, particularly for resolution levels >= 5.
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Ventana: treat as normal TIFF if no scanned areas defined
.bif files may be post-processed to remove overlaps and overlap metadata. These files will have the same IFD order and magnification metadata, but do not need any of the logic to recalculate image sizes and tile positions. Conflicts: components/formats-gpl/src/loci/formats/in/VentanaReader.java
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Commits on Mar 30, 2019
Commits on Apr 1, 2019
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Check for "iScan" in the XML tag during isThisType
This should prevent incorrect detection of other TIFF files that have tag 700.