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

There was an off-by-one error in the setting of the extent.

Change-Id: I1818184845a11bc7cbf560e4bfb270a943c8a8ac

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

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

Change-Id: I6546ff164baca86afb1a73b896dd10b1bce2c005

Change-Id: I5f19b101063e1a25d4f5db5c4356ce5efffbd90d

Change-Id: If92879d67d11dfc5965ef42a8c173539801b3c98

Change-Id: I10a54acbd076e055d8071414f2fff1ebafe1653d

Change-Id: Ie3a7d94877dd70b82bc86b20816980013956c9ef

As Robert Maynard pointed out we already control for this in the
CanRead function, and so there is no need to repeatedly verify this
on every volume or tile read.

Change-Id: I47247928503c3e070a3905950fd726a2392c281a

Updating progress per page seems to give reasonable updates.

Change-Id: I142f5e18fad8294df2367d82bea171567c005fa5

Fairly big refactoring of the TIFF reader, use templated methods in
many more places, avoid loss of type after it is determined, added
support for reading in 32 bit float TIFFs.

Change-Id: I4abf61179461acfa04c2c17c4e6d20467587c984

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

Using just long as the type will fail on window machine where long
size is 4 unlike Posix machines where it is 8. So we use the vtkTypeInt64
type which is always 8 bytes long.

Change-Id: Ib61d5e1860c411e44153904b497c525f392d2f32

Comment reason for <string> inclusion.

Change-Id: I7e0b1d7bd52a3ee66f5d078f330520bb7e6461a2

Change-Id: Icc81419ba319821ae5fc68bc8db3eadc2db5f818

Change-Id: I92102c8ac0609f80308f6954f6bc89aabf42e963

The documentation now contains the default for
vtkDelimitedTextReader::HaveHeaders (false).

Change-Id: Ie97f17d427d92243e710a0d6b85d8f6ffc67a6ea

Now that <sstream> is not included we need <string> to get std::string
when compiling Java wrapper sources.

Change-Id: I5b36410f8bdb2e13c497b0adaa11e95142fd56a0

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

Change-Id: I69137fd0b90ae9f5194af99995df6b1af06d1b41

Change-Id: I16387bcb7a1f5198f5394a203a0345332740a147

Combine PhyloXML reader & writer tests into a single test,
and make it more thorough.

Change-Id: Ibb32ece7de203269a8508cb06eee91d94706f197

This class allows us to read a PhyloXML file to generate a
vtkTree.  This commit also contains corresponding change to
vtkPhyloXMLTreeWriter.

Change-Id: Idd7a7a997e24f0c751ee51ee8e2e9eb4c9c05c7a

Extend this class so that it can read from either a file or a
string.

Change-Id: Ida093f0c4c44896ed59da96b8950e7ffa2b6351b

Change-Id: I6c20eb8650e2b079c8b1f581c9727a3d8205087a

Change-Id: I760f95e9374d00f619d273e515a7bc62b115c5b4

Prevent user input from blowing past the fourcc storage on the stack.

Change-Id: I7bcb92257f082bae8611a65b8f018ea9477c4dbe

The RequestData return value of 0 means an error and make the actual
reader implementations return a boolean.

Change-Id: I3caf27782fb34e5e5474f40ef8d466bda61cd12c

Change-Id: I30268a666f3b3dd65ff8085524007d2ab57d357f

Change-Id: I38a189e6af609836a846d892050440e69473a9b7

The STL format only supports triangles and previously, it just truncated
polygons silently. Cause an error to occur when this happens so that
users know.

Change-Id: I9c2f96d887074943130a8442d6796cb0c2ce1bbf

The PhyloXML specification indicates that references should
match the following regular expression pattern:

[a-zA-Z0-9_]+:[a-zA-Z0-9_\.\-\s]+

In order to do so, we now prepend "VTK:" to the beginning of the
array name.

Change-Id: Ie898e19dc10ec6edd2b67a5b493f55521e15c63d

A test failure was introduced by the commit "BUG: fix some xdmf writer crashes".
This new patch reverts the change which caused the failure.

Change-Id: Ifbb3a68b14f0c5a5cd390fc68d9a50668ca60ac8

subclasses of vtkXMLWriter should now call OpenStream & CloseStream
as opposed to OpenFile & CloseFile.

Change-Id: I39ccdc711d07e96763fc941b5fcd80b1da6b38c5

This commit enables vtkXMLWriter and its subclasses to write
their output to a string instead of a file.

Change-Id: Idff93039f9536379e3ef9abad6ea4ce18b4f2a60

The point and cell arrays were being enabled/disabled after they
were supposed to which resulted in potentially having the wrong
arrays read in.

Change-Id: Ic0435bcf6447260fe76ddc32b47719d7262fca44

This is an improvement over our previous approach of constructing
the path to the baseilne file from the testing directory.

Change-Id: I2dc0e1354c381ff770475ff2ab7f561b0122e582

Forgot to add the new Baseline directory for IO/Infovis tests.
Hopefully this fixes my failing TestPhyloXMLTreeWriter test.

Change-Id: I153e3b280b27888122d2c09d4eddc18362e6382d

This test now compares its output against a baseline .xml file.

Change-Id: I1e612a1375fc933947228cfa03f16a27aab3bca4