Initial commit
Various tools to inspect and reorient nifti files:
nii2snapshot.py creates an quick overview of the contents of a nifti file.
nii2svg.py (incomplete) converts a nifti files into a series of png slices, ready for processing by an png2svg converter.
nii_reorient.py swaps dimensions of a nifti file that violates the standard by permuting the affine matrices stored in the header.
common_nifti_errors.txt describes common violations of the Nifti1 standard.
modified nii_reorient to use ijk instead of xyz
Small textual improvements to common_nifti_errors
Renamed nii2svg to nii2png, and fixed minor bugs.
dims = img.shape was before apply_orientation
PIL was still used, now eliminated
Merge branch 'master' of https://github.com/INCF/Vectorization-of-brain-atlases
Adds routines to inspect and reorient nifti files.
use relative paths in html output of nii2inspect
Minor fix in inspection html
fix transparency in nii_inspect.html
Added 3rd layer to nifti inspection tool
Added title to each layer in  nii2inspect
New arguments for nii2inspect; can now specify color range
Multiple -i inputs should now work
Added toggle button to nii_inspect viewer
Minor fix in nii2inspect, replace is by ==
Include nifti source in html
Added possibility to specify alpha-#RGB colormap
fixes bug in hex2rgb
Added percentile parameter to layer specification, to improve brightness of rescaled images.