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  1. 07 Jul, 2015 1 commit
  2. 18 Apr, 2014 1 commit
    • Zack Galbreath's avatar
      break vtkRCalculatorFilter's input/output symmetry · ea356a14
      Zack Galbreath authored
      Before this commit, vtkRCalculatorFilter produced the same type
      of output as its input.  This is no longer the case.  For example,
      you can now run an R script that takes one table as input
      and produces two trees as output.  A test is included for this
      new functionality.
      
      This commit also makes vtkRAdapter::RToVTKTree() more robust.
      Previously, we assumed that the elements in the R Tree would
      appear in a certain order, but apparently that is not guaranteed
      to be true.  We now parse these elements in whatever order they
      appear.  While I was modifying this function, I also cleaned it up
      so it should now adhere to VTK's coding style.
      
      Change-Id: I988361ee8e6788f6f51e0c930fc52df50d1b2912
      ea356a14
  3. 15 Apr, 2014 1 commit
    • Zack Galbreath's avatar
      preserve R data.frame row names · c06dd72d
      Zack Galbreath authored
      When converting from an R data.frame to a vtkTable, store their
      row names (if any) in a string column at the beginning of the table.
      
      Change-Id: Ie9bc73a8c83ae7aec46ce05bc0de849a1c0f3da2
      c06dd72d
  4. 28 Mar, 2014 1 commit
    • Zack Galbreath's avatar
      copy row names from R to vtkTable · 48341cd5
      Zack Galbreath authored
      Since vtkTable does not have a concept of row names, we add a
      vtkStringArray containing the names as the first column of the
      vtkTable.
      
      Change-Id: I2c9e20ed2c1d9cc21205e137ce9b9cfedd02a816
      48341cd5
  5. 18 Nov, 2013 1 commit
    • Zack Galbreath's avatar
      fix failing RCalculator tests · ca924e77
      Zack Galbreath authored
      This commit resolves some issues that lingered after 5bd3962d.
      There were still a few spots in vtkRAdapter where we compensated
      for an extra root node.  This is now fixed.  The tree tests in
      this module also had to be updated now that VTK trees & R trees
      contain the same number of vertices and edges.
      
      Change-Id: I624c6e23b08146f91d3141aded8ccf380d9f6538
      ca924e77
  6. 13 Nov, 2013 1 commit
    • Zack Galbreath's avatar
      fix bug in vtkRAdapter::VTKTreeToR(vtkTree* tree) · 5bd3962d
      Zack Galbreath authored
      When this method was originally written it contained logic to
      skip an extra root node in the vtkTree as it translated it into
      an R variable.  More recently, I discovered that this extra root
      node was being created by a bug in vtkNewickTreeReader.  Now that
      the bug in the reader has been fixed, we need to eliminate this
      "skip root node" logic from vtkRAdapter so that it will continue
      to function as it has in the past.
      
      Change-Id: Id269a91df7cb7e88f39a9e0bf92fa010a3a0b7af
      5bd3962d
  7. 01 Sep, 2013 1 commit
  8. 27 Aug, 2013 1 commit
  9. 31 Jul, 2013 1 commit
    • Chris Harris's avatar
      Fix assert in vtkRAdapter · 43d4a38b
      Chris Harris authored
      907df317 introduced a bug that would allow
      nodeWeights->GetValue(...) to be called if parent is
      -1, move this code into the protected if block.
      
      Change-Id: I9838f59dbb8b571f75ac9eb38f33114f4de45eaf
      43d4a38b
  10. 15 Jul, 2013 1 commit
    • Zack Galbreath's avatar
      change leaf node display behavior · 1b0150a4
      Zack Galbreath authored
      Prior to this commit, leaf nodes were extended so that they all
      lined up vertically.  The motivation behind this behavior was
      to make it easy to see which leaf nodes correponded to each
      row in the heatmap.
      
      The problem with this approach is that it obscured information
      about how long these leaf nodes actually are.  Starting with this
      commit, the actual length of the leaf nodes is now drawn in black
      by default (the same as the rest of the tree).  The leaf nodes are
      still extended as before, but this extra length is now drawn in grey.
      
      This extension of the leaf nodes is also now a toggleable behavior.
      The options are always extend leaf nodes, never extend leaf nodes,
      or only extend leaf nodes if a heatmap is also loaded.  This latter
      option is the default.
      
      This commit also introduces two new public member functions: GetSize
      and GetCenter.  These functions make it easier to center this item
      within a scene in an end-user application.
      
      Change-Id: I11576b8822de2c915a6edb36c80c4721661aa317
      1b0150a4
  11. 09 May, 2013 1 commit
    • Zack Galbreath's avatar
      improve performance when reading a large Newick tree · 907df317
      Zack Galbreath authored
      Use vtkTreeDFSIterator when calculating the node weights of a tree
      ready by vtkNewickTreeReader.  For a sample tree with 63498 vertices,
      this change improves read time from 70.47s to 4.14s
      
      Change-Id: I0e35ff89ce207657a958cf606a85984aa8ee3de0
      907df317
  12. 18 Apr, 2013 2 commits
    • Zack Galbreath's avatar
      minor cleanup · 63533d6d
      Zack Galbreath authored
      remove debug message, plug memory leak
      
      Change-Id: If9fc08f0e046bcf89c0d14efc377b12d1a278605
      63533d6d
    • Zack Galbreath's avatar
      create another VertexData array in RToVTKTree · 833aadb5
      Zack Galbreath authored
      The "true node weight" array is also created when we read in a tree
      using the vtkNewickTreeReader.  This array is currently the best
      basis of comparison that we have for the vtkTreeDifferenceFilter.
      
      Change-Id: Iae7f8830f0c611d1aaca957e8a0651426d171da8
      833aadb5
  13. 13 Feb, 2013 1 commit
    • Zack Galbreath's avatar
      Fix memory leak when getting a tree from RCalculatorFilter's output · 3fee36a7
      Zack Galbreath authored
      This commit updates vtkRAdapter::RToVTKTree() to match the memory
      management strategy used in vtkRAdapter::RToVTKTable().  This commit
      also removes the deletion of the vtkTree in TestRInterface, as this
      is rendered inappropriate by the previously mentioned change.
      
      Change-Id: I764c9d28199d7b5421383947567cd37a93dbdec3
      3fee36a7
  14. 21 Dec, 2012 3 commits
  15. 28 Sep, 2012 1 commit
    • Xiaoxiao Liu's avatar
      Enable vtkTree I/O with R and multiple inputs in vtkRCalculaterFilter. · 2dc9be8e
      Xiaoxiao Liu authored
      1: Implemented the conversion between a
      R phylo tree and a VTKTree.
      
      A R "phylo" tree is a list of 5 elements, including:
      edge, Nnode,edge.length, tip.label, node.label.
      
      The indexing convension of the vertices of a tree is
      different between a "phylo" tree and the vtk tree.
      
      2: Modified the vtkRCalculaterFilter so that it can take
      in multipe input data types.For example,now you could add
      a table, a tree and an array to the input port 0. The filter
      will convert all vtk data inputs into R variables before
      running the RScripts. For now, the ouput number remains to be
      one. In the future, further modifications are needed to allow
      multiple outputs.
      
      Change-Id: Iba030e0d207c204aacec1e3058fb60bc954ffea0
      2dc9be8e
  16. 09 Apr, 2012 2 commits
    • VTK Developers's avatar
      Remove trailing whitespace from all source files · 2d323fc4
      VTK Developers authored and Brad King's avatar Brad King committed
      Exclude ThirdParty, Utilities/MetaIO, and Utilities/KWSys as these
      are maintained outside VTK.
      
      Co-Author: Marcus D. Hanwell <marcus.hanwell@kitware.com>
      Co-Author: Chris Harris <chris.harris@kitware.com>
      Co-Author: Brad King <brad.king@kitware.com>
      2d323fc4
    • VTK Developers's avatar
      Modularize VTK tree layout · cdd4d6fd
      VTK Developers authored and Brad King's avatar Brad King committed
      Move source files from their former monolithic VTK location to their new
      location in modular VTK without modification.  This preserves enough
      information for "git blame -M" and "git log --follow" to connect
      modularized VTK files to their original location and history.
      
      Co-Author: Marcus D. Hanwell <marcus.hanwell@kitware.com>
      Co-Author: Chris Harris <chris.harris@kitware.com>
      Co-Author: Brad King <brad.king@kitware.com>
      Co-Author: Nikhil Shetty <nikhil.shetty@kitware.com>
      cdd4d6fd
  17. 08 Mar, 2012 1 commit
    • David Gobbi's avatar
      COMP: Fix signed/unsigned and fread warnings in R interface. · 51fb84f0
      David Gobbi authored
      Fix the counter types used for iterating over arrays to avoid
      signed/unsigned errors.  Check the return value from fread()
      calls to verify that script reads are successful.  Remove the
      unused variable "path2" from vtkRInterface.cxx.
      
      Change-Id: Ic717bc0fd2bea7cb5be0785c89aa347bb5211ff1
      51fb84f0
  18. 13 Dec, 2011 1 commit
  19. 20 May, 2010 1 commit
    • Mark Olesen's avatar
      Remove vtk(Cxx|Type)RevisionMacro · ecbbf7f7
      Mark Olesen authored and Brad King's avatar Brad King committed
      The CVS $Revision$ keyword replacement will no longer maintain these
      macros automatically.  They were used only to implement CollectRevisions
      and vtkObjectBase::PrintRevisions, an API that was never used.
      
      Automated as follows:
      
        pass 0:
        catch templates
        ---------------
        $ git grep 'vtk\(Cxx\|Type\)RevisionMacro' | grep '<'
      
        pass 1:
        main changes
        ---------------
        $ git grep -l '^vtkCxxRevisionMacro' | while read file; do
          echo "$file" 1>&2
          perl -i -ne 'print unless (/^vtkCxxRevisionMacro/ and /\)/)' $file
        done
        $ git grep -l -e 'vtkTypeRevisionMacro(' | while read file; do
          echo "$file" 1>&2
          perl -i -pe 's/vtkTypeRevisionMacro/vtkTypeMacro/g' $file
        done
      
        pass 2:
        verify
        ---------------
        $ git grep 'vtk\(Cxx\|Type\)RevisionMacro'
      
      Fixed multi-line vtkCxxRevisionMacro and templates by hand.
      ecbbf7f7
  20. 23 Apr, 2010 1 commit
    • Mark Olesen's avatar
      Remove vtk(Cxx|Type)RevisionMacro · 19c55e0e
      Mark Olesen authored and Brad King's avatar Brad King committed
      The CVS $Revision$ keyword replacement will no longer maintain these
      macros automatically.  They were used only to implement CollectRevisions
      and vtkObjectBase::PrintRevisions, an API that was never used.
      
      Automated as follows:
      
        pass 0:
        catch templates
        ---------------
        $ git grep 'vtk\(Cxx\|Type\)RevisionMacro' | grep '<'
      
        pass 1:
        main changes
        ---------------
        $ git grep -l '^vtkCxxRevisionMacro' | while read file; do
          echo "$file" 1>&2
          perl -i -ne 'print unless (/^vtkCxxRevisionMacro/ and /\)/)' $file
        done
        $ git grep -l -e 'vtkTypeRevisionMacro(' | while read file; do
          echo "$file" 1>&2
          perl -i -pe 's/vtkTypeRevisionMacro/vtkTypeMacro/g' $file
        done
      
        pass 2:
        verify
        ---------------
        $ git grep 'vtk\(Cxx\|Type\)RevisionMacro'
      
      Fixed multi-line vtkCxxRevisionMacro and templates by hand.
      19c55e0e
  21. 12 Apr, 2010 1 commit
  22. 24 Mar, 2010 1 commit
  23. 17 Feb, 2010 1 commit
  24. 09 Feb, 2010 2 commits
  25. 04 Feb, 2010 1 commit
  26. 29 Jan, 2010 1 commit
    • Thomas Otahal's avatar
      · 61c885d8
      Thomas Otahal authored
      ENH:  Added R Array type for conversions to vtkArray.
      61c885d8
  27. 20 Jan, 2010 1 commit
  28. 14 Dec, 2009 1 commit
    • Thomas Otahal's avatar
      · f48fbab2
      Thomas Otahal authored
      ENH:  Added files and unit tests in VTK/Graphics for Matlab and Gnu R integration with VTK.  Added new advanced CMake options VTK_USE_MATLAB_MEX and VTK_USE_GNU_R to enable builds with Matlab and R.  Building the integration code requires a Matlab installation or an installation of GNU R compiled from source.  The integration files will be compiled with the vtkGraphics library.  Unit tests are located in VTK/Graphics/Testing/Cxx.  Python examples are located in VTK/Examples/Infovis/Python.
      f48fbab2