1. 21 May, 2014 5 commits
    • Berk Geveci's avatar
      Fixed compiler warnings. · a4c8e855
      Berk Geveci authored
      Change-Id: I80d4dbda38c7a6d83d6ba3fadeb81cce1154a1b1
      a4c8e855
    • Berk Geveci's avatar
      Fixed legacy parallel reader and writer. · 10c6913a
      Berk Geveci authored
      To work with the new pipeline changes.
      
      Change-Id: Ic5c8ac86026999f79924d8e61b10fbcb18286bb8
      10c6913a
    • Berk Geveci's avatar
      Cleaned up and fixed transmit filters for structured data. · 24a324ef
      Berk Geveci authored
      Change-Id: I7e5c55259159752882c8ae056e08f9bec12b3c02
      24a324ef
    • Berk Geveci's avatar
      Update the XML readers and writers to work with pipeline changes. · 32cf800f
      Berk Geveci authored
      The XML readers and writers, both parallel and serial, now work
      with the pipeline changes. Now, all writers work with pieces
      even though the structured ones can handle asking for a sub-
      extent.
      
      Change-Id: I9f757ba12a3b9fb84e141506dacadad608eb8b99
      32cf800f
    • Berk Geveci's avatar
      Refactored how pieces and extents are handled. · 1a0b4e9d
      Berk Geveci authored
      Refactoring the way VTK goes between piece and structured
      extents. Before, extent translators were used when the pipeline
      moved from structured to unstructured data converting piece
      request to extent request. This caused many problems with filters
      that altered extents, mainly a lot of redundant IO due to
      repartitioning of different extents. This became extremely
      cumbersome to manage when running distributed. The new behavior
      pushes the extent translation all to way to the readers and
      only when readers are able to read a subset. This works much
      better. The only downside is that filters need to be able to
      handle data extents different than update extents. Most filters
      can do this but many imaging filters cannot. Those that are
      needed in parallel will have to be updated.
      
      As part of this work, I also removed MAXIMUM_NUMBER_OF_PIECES
      and added CAN_HANDLE_PIECE_REQUEST. MAXIMUM_NUMBER_OF_PIECES had
      reduced to being a boolean. 1 for serial sources, -1 for parallel
      sources. I removed it and added a CAN_HANDLE_PIECE_REQUEST instead.
      This key, produced by a source, tells the executive that a source is
      able to handle piece request. It is a source only key produced in
      RequestInformation and is not propagated downstream. If this key is
      not present, the executive will only execute the source for piece 0
      to produce the entire data. It is then up to the user to add a filter
      that splits the data for other piece requests. The only exception to
      this is when CAN_PRODUCE_SUB_EXTENT is present, in which case the
      executive will split using an extent translator AT THE source - not
      downstream.
      
      Conflicts:
      	Filters/FlowPaths/vtkParticleTracerBase.cxx
      
      Change-Id: I8db4040289ff87331adeecded4a738313d9b52df
      1a0b4e9d
  2. 06 May, 2014 1 commit
    • David Gobbi's avatar
      NIFTI makes IOImage module depend on vtkzlib. · 1f777440
      David Gobbi authored
      This dependency has to be stated explicitly.  This error wasn't caught
      immediately because, on most sytems, vtkzlib is linked transitively via
      vtktiff and vtkpng.
      
      Change-Id: I36408557a7eed266fe05cdc891fc75dc1259502e
      1f777440
  3. 04 May, 2014 1 commit
  4. 01 May, 2014 1 commit
    • David Gobbi's avatar
      Add reader/writer for NIFTIv1 and NIFTIv2 files. · e7aa61da
      David Gobbi authored
      This patch adds support for reading and writing NIFTI files, as well
      as full access to the NIFTI header.  Versions 1 and 2 of the NIFTI
      header are supported, and the reader can also be used to read Analyze 7.5
      files, though the only Analyze header elements that are supported are the
      ones that overlap with NIFTI.  Automatic compression and expansion for
      gzipped files is also provided whenever the filename ends with a .gz
      extension.
      
      Change-Id: Iead3afb1a65d8c01aa52f3ca55c6da2f08703375
      e7aa61da
  5. 30 Apr, 2014 3 commits
    • David Gobbi's avatar
      Two fixes for certain lsm (zeiss) tiff images. · 7ff8bfd0
      David Gobbi authored
      The first fix is that some zeiss images set PlanarConfig to "SEPARATE"
      (i.e. separate color planes) even when NumberOfSamples is 1.  When the
      number of samples is one, the PlanarConfig can be safely ignored.
      
      The second fix is that ReadVolume assumed that the number of slices was
      always equal to NumberOfPages, which was in conflict with ExecuteInformation
      which set the number of slices to SubFiles if SubFiles > 0 (cf line 505).
      This caused a crash, because ReadVolume was reading more data than the
      reader had allocated space for.
      
      Change-Id: I822e45a53c210b5edebfe8ce27443fe1434110ba
      7ff8bfd0
    • George Zagaris's avatar
      BUGFIX: Fix issue with unigrid enzo datasets · df25648b
      George Zagaris authored
      Fixed issued with unigrid enzo datasets. The reader
      was calculating number of levels to be 0, which was
      leading to a segfault. Added code to detect unigrid
      datasets and fixed the issue by setting the number
      of levels to 1.
      
      Change-Id: Ie9f1fbe8c3c38c69e5761b357256be9531ed10f3
      df25648b
    • David Gobbi's avatar
      Fix the extent for tiled tiff files. · 0fe573e8
      David Gobbi authored
      There was an off-by-one error in the setting of the extent.
      
      Change-Id: I1818184845a11bc7cbf560e4bfb270a943c8a8ac
      0fe573e8
  6. 23 Apr, 2014 1 commit
    • Brad King's avatar
      Use vtkMPI.cmake helper for all module MPI tests · c05001df
      Brad King authored
      In commit cd4fc15a (Rewrite the testing macros, 2014-03-14)
      the vtk_test_mpi_executable() helper was introduced to add
      MPI tests.  It depends on the vtk_mpi_link() helper in the
      vtkMPI module.  Include the latter in all test CMakeLists.txt
      files that add MPI tests.
      
      Change-Id: Ifecc7c6b1bf856a8f66905bfb2d69e22b5de3aac
      c05001df
  7. 17 Apr, 2014 1 commit
    • Marcus D. Hanwell's avatar
      Copy simple TIFF images into buffers more directly · 4e060c24
      Marcus D. Hanwell authored
      If we have simple, single component, tightly-packed images then
      copy them directly into the allocated buffer. If we are clipping, use
      memcpy to just copy the subset requested. This is primarily aimed at
      accelerating the load times for TIFF volumes. Thanks to Robert
      Maynard for the suggested simplications in the templated image
      function.
      
      Change-Id: I6c3b10a019fc892b1e1bbbce32841e7f946eb995
      4e060c24
  8. 16 Apr, 2014 4 commits
  9. 15 Apr, 2014 1 commit
  10. 11 Apr, 2014 3 commits
  11. 26 Mar, 2014 1 commit
    • Ben Boeckel's avatar
      Exodus: Always attach the title to the output fields · e073d6de
      Ben Boeckel authored
      The title is a statically-sized array, not a raw pointer, so it is
      always non-NULL. Always attach the title since we don't need to worry
      about NULL-dereferences.
      
      Change-Id: I6c855cf4d8a04dd206dcb983555a2bcb01a4179a
      e073d6de
  12. 24 Mar, 2014 1 commit
  13. 13 Mar, 2014 6 commits
    • Brad King's avatar
      IO/XML: Fix HeaderTest for this module · f2a2eeab
      Brad King authored
      Comment reason for <string> inclusion.
      
      Change-Id: I7e0b1d7bd52a3ee66f5d078f330520bb7e6461a2
      f2a2eeab
    • Robert Maynard's avatar
      Correct warnings about negative unsigned constant values. · d353840f
      Robert Maynard authored
      Change-Id: Icc81419ba319821ae5fc68bc8db3eadc2db5f818
      d353840f
    • Dan Lipsa's avatar
      Remove debugging printouts. · 1d7c4549
      Dan Lipsa authored
      Change-Id: I92102c8ac0609f80308f6954f6bc89aabf42e963
      1d7c4549
    • Dan Lipsa's avatar
      Update documentation. · 9ac19b71
      Dan Lipsa authored
      The documentation now contains the default for
      vtkDelimitedTextReader::HaveHeaders (false).
      
      Change-Id: Ie97f17d427d92243e710a0d6b85d8f6ffc67a6ea
      9ac19b71
    • Brad King's avatar
      IO/XML: Add missing <string> include · 4327fceb
      Brad King authored
      Now that <sstream> is not included we need <string> to get std::string
      when compiling Java wrapper sources.
      
      Change-Id: I5b36410f8bdb2e13c497b0adaa11e95142fd56a0
      4327fceb
    • Brad King's avatar
      IO/XML: Remove unnecessary <sstream> include · d8a74423
      Brad King authored
      The VTK standard headers include <iosfwd> and make std::istringstream
      available for use as an incomplete type.  That is all vtkXMLReader.h
      needs.  Remove the extra <sstream> include.
      
      In particular, by including it before the VTK headers it causes system
      headers to be included with inconsistent Large File Support definitions
      on AIX, leading to runtime shared library unresolved symbols.  Remove
      the inclusion to fix this.
      
      Change-Id: I78ec9efae24c8f721f079ab8946afcde413fe17f
      d8a74423
  14. 10 Mar, 2014 1 commit
  15. 06 Mar, 2014 4 commits
  16. 05 Mar, 2014 1 commit
  17. 04 Mar, 2014 2 commits
  18. 28 Feb, 2014 3 commits