PYR: SHA1 handling is broken

[jamoore]

Traditionally, sha1 generation has been plane (i.e. row) based. For pyramids, it will need to be tile based. Since this isn't specified anywhere, the change should be transparent for users. The logic may should be pushed down into bioformats so that any reader will provide a sha1 in the appropriate way.

[jmoore]

BfPixelWrapper, for example, is calculating by timepoint (though ByPyramidPixelBuffer disallows getTimepoint, it is unwittingly using it itself via the delegate).

    public byte[] getMessageDigest() throws IOException {
       MessageDigest md;
       try {
           md = MessageDigest.getInstance("SHA-1");
       } catch (NoSuchAlgorithmException e) {
           throw new RuntimeException(
                   "Required SHA-1 message digest algorithm unavailable.");
       }
       for (int t = 0; t < sizeT; t++) {
           try {
               byte[] buffer = new byte[timepointSize];
               getTimepoint(t,buffer);
               md.update(ByteBuffer.wrap(buffer));
           } catch (DimensionsOutOfBoundsException e) {
               throw new RuntimeException(e);
           }
       }
       return md.digest();
   }

[jburel]

Moved from sprint 2011-04-21 (10)

[jburel]

Moved from sprint 2011-05-19 (12)

[jburel]

Moved from sprint 2011-06-02 (13)

[jmoore <josh@…>]

(In [5ff290a5eafaee60ec7211e79c39888e34615188/ome.git] on branch develop) Adding forEachTile to omero.client in OmeroJava (See #4927, #5755)

[jmoore <josh@…>]

(In [dbe2b7240d3ffe7cb6968d997da255846e56ddb9/ome.git] on branch develop) Adding forEachTile to omero.client in OmeroPy (See #4927)

[Will Moore <will@…>]

(In [70fabe9f09d21eec352a019308f4db3779b2bddb/ome.git] on branch develop) Adding counter and delay to Python integration testRomioToPyramid. See #4927

[jmoore <josh@…>]

(In [bdf988d4c389a3ec42a5410fe5f4cc9c54079bd1/ome.git] on branch develop) Partial revert of [4ea06983d312c06a5e1c61175afac01884a31b0c/ome.git]

Changes to omero.client were inadvertent (See #4927)

[jmoore <josh@…>]

(In [7f4b2fe42b6b772a2ac0b25b8c6dd614127cdcd0/ome.git] on branch develop) Move OmeroJava and OmeroPy omero.client.forEachTile to TileLoop? classes (See #4927)

[jmoore <josh@…>]

(In [23f73f491901c35cca77a1aeda89cc3efdb350b5/ome.git] on branch develop) Add TileLoop to OmeroCpp (Fix #4927)

[jmoore]

Rather than completely solve SHA1s the decision was to specify in all languages how to loop over the data. The previous (closing) commit finally added support for OmeroCpp (mildly tested).