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Add reader for Ventana .bif files #3336

Merged
merged 27 commits into from Jul 3, 2019
Commits on Mar 29, 2019
  1. Progress on tile stitching for the full resolution image

    melissalinkert committed Oct 12, 2018
    Not done yet, as the overlaps are still not quite right.  This is closer
    than the previous version with no overlap calculation though.
  2. Average a subset of recorded overlaps instead of using overlap list

    melissalinkert committed Nov 15, 2018
    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.
  3. Add "ventana.split_tiles" boolean option

    melissalinkert committed Nov 15, 2018
    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.
  4. Fix compile errors

    melissalinkert committed Feb 27, 2019
  5. Ventana: adjust XY size to match AOI bounds

    melissalinkert committed Feb 21, 2019
    Conflicts:
    	components/formats-gpl/src/loci/formats/in/VentanaReader.java
  6. Adjust XY coordinate calculation for low resolution tiles

    melissalinkert committed Feb 25, 2019
    Changing the rounding strategy results in smoother stitching,
    particularly for resolution levels >= 5.
  7. Ventana: treat as normal TIFF if no scanned areas defined

    melissalinkert committed Mar 25, 2019
    .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
Commits on Mar 30, 2019
  1. Fix warnings

    melissalinkert committed Mar 30, 2019
Commits on Apr 1, 2019
  1. Check for "iScan" in the XML tag during isThisType

    melissalinkert committed Apr 1, 2019
    This should prevent incorrect detection of other TIFF files that have tag 700.
Commits on Apr 17, 2019
  1. TIFF: reduce array allocations and unpacking method calls

    melissalinkert committed Apr 9, 2019
Commits on Apr 25, 2019
  1. Fix typo in setting up pixel unpacking for <8 bit data

    melissalinkert committed Apr 25, 2019
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