File	Date	Author	Commit
src	2014-09-01	Gert Wollny	[072ff6] update copyright year
.gitignore	2013-10-16	Gert Wollny	[d7a954] update ignore files
AUTHORS	2012-03-26	Gert Wollny	[8c54f1] initial checkin
COPYING	2012-05-18	Gert Wollny	[9d3970] add copyright info
ChangeLog	2015-01-08	Gert Wollny	[562ac9] remove spaces
MANIFEST.in	2013-10-23	Gert Wollny	[0660c0] correctly add header files to source distribution
README	2013-12-04	Gert Wollny	[882630] remove the python tools as they are not python3
setup.py	2015-01-07	Gert Wollny	[f70184] update version and name of module

Read Me

This is the python interface for the MIA library. It uses numpy to 
represent images, and currently, filters and image registration is 
supported. 

  Compiling the interface:

The build system utilizes python distutils. To compile the interface 
the compiler must support the -std=c++11 compiler flag. 
Building the interface then build down to running 

  python setup.py build 

Note, that you wil need mia >= 2.0.10 to be installed. 


  Using the python interface: 

Given that MyImage is a 2D or 3D numpy array of scalar values, one may 
run a filter chain like 
 
  import mia

  MyFilteredImage = mia.filter(MyImage, ["filter1:param1=a", 
                                     "filter2:param1=b,param2=c", ...])

For the availabe filters see the user reference of MIA.


Similarly, the image registration can be run with images Moving and Reference, 
using a spline based transformation with a coefficient rate of 5 pixels, 2 
multi-resolution levels and an nlopt based optimizer: 

  import mia
  Registered = mia.register_images(src=Moving, ref=Reference, 
     transform="spline:rate=5", cost=["image:cost=ssd", "divcurl:weight=10.0"],
     mglevels=2, optimizer="nlopt:opt=ld-var1,xtola=0.001,ftolr=0.001,maxiter=300")


The result image is stored in Registered. Currently, the transformation is lost.