are now sent by email.

Patch by Jeff Lovelace

there are now three startup files; ost_startup.py (former init_cl.py) initializes non-gui ost; dng_startup (former init.py) initializes dng; and gosty_startup initializes gosty (some issues remain what to put into dng_startup as opposed to gosty_startup). also, files are now properly placed into site-packages/ost (on osx and linux)

moved scene.Export to python layer to allow differentiated argument handling; more fixes to glx framebuffer memory handling

yet.

Conflicts:
	CMakeLists.txt

Conflicts:
	CMakeLists.txt

Marco Biasini authored 12 years ago and Bienchen committed 12 years ago

Mainly written by Valerio, with a few tweaks by me

parameters of RenumberChain function.

with the requested editor. Attention: Interface of RenumberChain has slightly
changed.

changed python unit tests to run with python instead of ost

Remarks
-------

Python unit tests using blast, clustalw or the compound lib where
skipped on my system. There might be still some missing imports in
these tests.

Changed in detail:
------------------

- removed DEPRECATED and unused code (slice and row pointers) in value holder
- switched from new allocatd array to std::vector
- removed explicit data initialization loop
- using size_t instead of unsigned int for memory allocation
- removed padding code
- removed try catch(...) statements
- added overflow check for big volumes
- optimized 3D index to linear index calculation
- removed physical extent for spatial domain (identical to logical extend not that padding is gone)
- switched FFT to out of place transforms

Benefits
--------

- memory for large images is correctly allocated
- if the memory can't be allocated an exception is thrown instead of crashing the program
- speed increase for FFT ca. 12% and for algorithms using direct value access (e.g. Stat) ca. 7%

Issues
-----

- FFTs are not out of place, leading to increased memory usage for c2c DFT backtransform and
  hc2r FFT/DFT backtransform (3x image size instead of 2x image size). If necessary it would
  be possible to add a fallback for these cases (i.e. catch bad_alloc for the tmp state) and
  do them in place in low memory conditions. Padding for the in-place transform could be added
  to the std::vector either at construction time or otherwise using reserve().