Change-Id: Id76d3bc545a64675a0820cb1d9b45c61a51efc6a

Change-Id: I24bf3b0959bf6e22543bb526b26d9fda14ab4c20

Change-Id: I80d4dbda38c7a6d83d6ba3fadeb81cce1154a1b1

To work with the new pipeline changes.

Change-Id: Ic5c8ac86026999f79924d8e61b10fbcb18286bb8

Change-Id: I7e5c55259159752882c8ae056e08f9bec12b3c02

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

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

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

Change-Id: I721d91a75a04f485a34aeed9fa04b154d892b1f8

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

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

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

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