ENH: Deprecated SetProgress and removed Modified call

SetProgress is now marked as deprecated because filters should not be
calling SetProgress directly but should be using
UpdateProgress instead.  We also avoid the use of the itkSetClampMacro
because that macro calls Modified on the filter, which will cause the
filter to rerun even if it doesn't need to.  Thus, we implement the
SetClampMacro directly without the call to Modified.

We also explicitly clamp the input argument to UpdateProgress to
ensure that the value lies between 0.0 and 1.0.

Change-Id: I0564082c15a9518dc5a6449e86e519b7ebe76458
BUG: Need to set 3rd dir cosine for DICOM images

DICOM images are always read in DCMTKImageIO as 3D even when they're
single-slice files. This is because DICOM slice files always have a
3D orientation. But DCMTKImageIO::ReadImageIO was only setting the
third direction cosine if the Z dimension was greater than 1.

This accidentally worked in many cases, as the 3rd dir cosine is
initialized to 0 0 1.  But in cases where another dir cosine is
0 0 N (or close to that), it makes for degenerate orientation
matrices.

Change-Id: I33cd39e3cd715bdddf3791cbbe08e562d2eb6088
Merge topic 'DeprecatedSetProgress'

230666c ENH: Deprecated SetProgress and removed Modified call
Merge topic 'DICOM_DIRCOSINES_BUG'

df53542 BUG: Need to set 3rd dir cosine for DICOM images